Starting phenix.real_space_refine
on Tue Mar 11 15:20:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y72_33651/03_2025/7y72_33651.cif"
  }
  resolution = 4.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   1.000
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      26      5.16       5
     C    3920      2.51       5
     N    1024      2.21       5
     O    1193      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6163
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1395
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1395
          Classifications: {'peptide': 174}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 164}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 1445
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 181, 1445
          Classifications: {'peptide': 181}
          Link IDs: {'PTRANS': 9, 'TRANS': 171}
    Chain: "P"
      Number of atoms: 1679
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1679
          Classifications: {'peptide': 219}
          Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 205}
    Chain: "O"
      Number of atoms: 1644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1644
          Classifications: {'peptide': 221}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 204}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   GLU O 155 " occ=0.71
      ... (7 atoms not shown)
      pdb=" OE2 GLU O 155 " occ=0.71
    residue:
      pdb=" N   VAL O 157 " occ=0.79
      ... (5 atoms not shown)
      pdb=" CG2 VAL O 157 " occ=0.79
    residue:
      pdb=" N   SER O 186 " occ=0.78
      ... (4 atoms not shown)
      pdb=" OG  SER O 186 " occ=0.78
    residue:
      pdb=" N   ARG O 217 " occ=0.78
      ... (9 atoms not shown)
      pdb=" NH2 ARG O 217 " occ=0.78
  Time building chain proxies: 4.80, per 1000 atoms: 0.78
  Number of scatterers: 6163
  At special positions: 0
  Unit cell: (98.345, 83.98, 119.34, 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      26     16.00
     O    1193      8.00
     N    1024      7.00
     C    3920      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS P  23 " - pdb=" SG  CYS P  93 " distance=2.04
    Simple disulfide: pdb=" SG  CYS P 139 " - pdb=" SG  CYS P 199 " distance=2.04
    Simple disulfide: pdb=" SG  CYS O  22 " - pdb=" SG  CYS O  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O 147 " - pdb=" SG  CYS O 203 " 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: 1.24
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1464

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 13 sheets defined
      9.7% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.612A  pdb=" N   SER A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 3.838A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 4.955A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.744A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.722A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 371
    Processing helix  chain 'C' and resid 383 through 390
      removed outlier: 4.345A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP C 389 " --> pdb=" O   LYS C 386 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 411
    Processing helix  chain 'P' and resid 126 through 133
      removed outlier: 3.654A  pdb=" N   GLY P 133 " --> pdb=" O   GLN P 129 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 61 through 64
      removed outlier: 3.640A  pdb=" N   LYS O  64 " --> pdb=" O   PRO O  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 61 through 64'
    Processing helix  chain 'O' and resid 86 through 90
    Processing helix  chain 'O' and resid 163 through 165
      No H-bonds generated for 'chain 'O' and resid 163 through 165'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358
      removed outlier: 3.921A  pdb=" N   ILE A 358 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ILE A 402 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.703A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   TYR C 380 " --> pdb=" O   GLY C 431 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   VAL C 433 " --> pdb=" O   LYS C 378 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   LYS C 378 " --> pdb=" O   VAL C 433 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'P' and resid 5 through 7
      removed outlier: 3.600A  pdb=" N   SER P  22 " --> pdb=" O   SER P   7 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   CYS P  23 " --> pdb=" O   PHE P  76 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   PHE P  76 " --> pdb=" O   CYS P  23 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   THR P  74 " --> pdb=" O   SER P  25 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   THR P  77 " --> pdb=" O   SER P  70 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   SER P  68 " --> pdb=" O   LYS P  79 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'P' and resid 10 through 13
      removed outlier: 6.242A  pdb=" N   LEU P  11 " --> pdb=" O   GLU P 110 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE P  53 " --> pdb=" O   TRP P  40 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU P  42 " --> pdb=" O   LEU P  51 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   LEU P  51 " --> pdb=" O   LEU P  42 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'P' and resid 119 through 123
      removed outlier: 3.527A  pdb=" N   SER P 119 " --> pdb=" O   ASN P 142 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL P 137 " --> pdb=" O   LEU P 184 " (cutoff:3.500A)
      removed outlier: 5.878A  pdb=" N   TYR P 178 " --> pdb=" O   ASN P 143 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'P' and resid 158 through 160
      removed outlier: 4.767A  pdb=" N   TRP P 153 " --> pdb=" O   GLN P 160 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LYS P 150 " --> pdb=" O   THR P 202 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   THR P 202 " --> pdb=" O   LYS P 150 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA P 198 " --> pdb=" O   LYS P 154 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS P 199 " --> pdb=" O   LYS P 212 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   LYS P 212 " --> pdb=" O   CYS P 199 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL P 201 " --> pdb=" O   VAL P 210 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   VAL P 210 " --> pdb=" O   VAL P 201 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'O' and resid 5 through 7
      removed outlier: 3.563A  pdb=" N   LEU O  80 " --> pdb=" O   LEU O  20 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   PHE O  78 " --> pdb=" O   CYS O  22 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'O' and resid 11 through 12
      removed outlier: 3.994A  pdb=" N   GLY O  49 " --> pdb=" O   TRP O  36 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG O  38 " --> pdb=" O   TRP O  47 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   TRP O  47 " --> pdb=" O   ARG O  38 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR O  50 " --> pdb=" O   ASN O  58 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASN O  58 " --> pdb=" O   TYR O  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'O' and resid 127 through 131
      removed outlier: 3.659A  pdb=" N   GLY O 146 " --> pdb=" O   LEU O 131 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA O 143 " --> pdb=" O   VAL O 191 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP O 151 " --> pdb=" O   TYR O 183 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TYR O 183 " --> pdb=" O   ASP O 151 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'O' and resid 127 through 131
      removed outlier: 3.659A  pdb=" N   GLY O 146 " --> pdb=" O   LEU O 131 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ALA O 143 " --> pdb=" O   VAL O 191 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP O 151 " --> pdb=" O   TYR O 183 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   TYR O 183 " --> pdb=" O   ASP O 151 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'O' and resid 158 through 161
      removed outlier: 3.982A  pdb=" N   THR O 158 " --> pdb=" O   ASN O 206 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   TYR O 201 " --> pdb=" O   VAL O 218 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   CYS O 203 " --> pdb=" O   LYS O 216 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS O 216 " --> pdb=" O   CYS O 203 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    396 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: 1.90

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1568
        1.33 -     1.45: 1340
        1.45 -     1.57: 3385
        1.57 -     1.69: 0
        1.69 -     1.82: 29
  Bond restraints: 6322
  Sorted by residual:
  bond pdb=" C   PHE C 486 "
       pdb=" O   PHE C 486 "
    ideal  model  delta    sigma   weight residual
    1.236  1.210  0.026 1.28e-02 6.10e+03 4.27e+00
  bond pdb=" C   GLU C 484 "
       pdb=" O   GLU C 484 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.025 1.26e-02 6.30e+03 3.87e+00
  bond pdb=" CA  PHE C 486 "
       pdb=" C   PHE C 486 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.026 1.43e-02 4.89e+03 3.39e+00
  bond pdb=" N   ALA O 121 "
       pdb=" CA  ALA O 121 "
    ideal  model  delta    sigma   weight residual
    1.454  1.478 -0.025 1.34e-02 5.57e+03 3.35e+00
  bond pdb=" N   ARG P 113 "
       pdb=" CA  ARG P 113 "
    ideal  model  delta    sigma   weight residual
    1.455  1.476 -0.021 1.18e-02 7.18e+03 3.13e+00
  ... (remaining 6317 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 8376
        1.79 -     3.58: 191
        3.58 -     5.37: 27
        5.37 -     7.15: 7
        7.15 -     8.94: 2
  Bond angle restraints: 8603
  Sorted by residual:
  angle pdb=" N   PHE C 486 "
        pdb=" CA  PHE C 486 "
        pdb=" C   PHE C 486 "
      ideal   model   delta    sigma   weight residual
     112.87  106.77    6.10 1.20e+00 6.94e-01 2.58e+01
  angle pdb=" C   SER A 443 "
        pdb=" N   LYS A 444 "
        pdb=" CA  LYS A 444 "
      ideal   model   delta    sigma   weight residual
     121.54  130.48   -8.94 1.91e+00 2.74e-01 2.19e+01
  angle pdb=" N   ARG P  66 "
        pdb=" CA  ARG P  66 "
        pdb=" C   ARG P  66 "
      ideal   model   delta    sigma   weight residual
     114.56  109.14    5.42 1.27e+00 6.20e-01 1.82e+01
  angle pdb=" N   GLY C 485 "
        pdb=" CA  GLY C 485 "
        pdb=" C   GLY C 485 "
      ideal   model   delta    sigma   weight residual
     112.73  117.62   -4.89 1.20e+00 6.94e-01 1.66e+01
  angle pdb=" N   ASN C 487 "
        pdb=" CA  ASN C 487 "
        pdb=" C   ASN C 487 "
      ideal   model   delta    sigma   weight residual
     110.80  118.59   -7.79 2.13e+00 2.20e-01 1.34e+01
  ... (remaining 8598 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 3420
       17.79 -    35.58: 265
       35.58 -    53.37: 46
       53.37 -    71.16: 8
       71.16 -    88.95: 6
  Dihedral angle restraints: 3745
    sinusoidal: 1441
      harmonic: 2304
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.65   44.35     1      1.00e+01 1.00e-02 2.74e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.05  -41.95     1      1.00e+01 1.00e-02 2.46e+01
  dihedral pdb=" CA  SER O 120 "
           pdb=" C   SER O 120 "
           pdb=" N   ALA O 121 "
           pdb=" CA  ALA O 121 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.36   20.64     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 3742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 693
       0.042 -    0.085: 154
       0.085 -    0.127: 84
       0.127 -    0.169: 5
       0.169 -    0.212: 2
  Chirality restraints: 938
  Sorted by residual:
  chirality pdb=" CA  ASN C 487 "
            pdb=" N   ASN C 487 "
            pdb=" C   ASN C 487 "
            pdb=" CB  ASN C 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  LEU O 102 "
            pdb=" N   LEU O 102 "
            pdb=" C   LEU O 102 "
            pdb=" CB  LEU O 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality pdb=" CA  ASN C 460 "
            pdb=" N   ASN C 460 "
            pdb=" C   ASN C 460 "
            pdb=" CB  ASN C 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.89e-01
  ... (remaining 935 not shown)

  Planarity restraints: 1111
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS P 112 "    0.020 2.00e-02 2.50e+03   4.01e-02 1.61e+01
        pdb=" C   LYS P 112 "   -0.069 2.00e-02 2.50e+03
        pdb=" O   LYS P 112 "    0.026 2.00e-02 2.50e+03
        pdb=" N   ARG P 113 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER O 120 "   -0.020 2.00e-02 2.50e+03   3.92e-02 1.54e+01
        pdb=" C   SER O 120 "    0.068 2.00e-02 2.50e+03
        pdb=" O   SER O 120 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   ALA O 121 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 484 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.50e+00
        pdb=" C   GLU C 484 "    0.047 2.00e-02 2.50e+03
        pdb=" O   GLU C 484 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLY C 485 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1108 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 546
        2.75 -     3.28: 5890
        3.28 -     3.82: 9254
        3.82 -     4.36: 10216
        4.36 -     4.90: 18204
  Nonbonded interactions: 44110
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 493 "
            pdb=" OD1 ASP P  75 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OG  SER A 349 "
            pdb=" O   LEU A 452 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   THR A 500 "
            pdb=" NE2 GLN A 506 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OG1 THR C 478 "
            pdb=" ND2 ASN C 487 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OE1 GLN A 414 "
            pdb=" ND2 ASN P  33 "
     model   vdw
     2.277 3.120
  ... (remaining 44105 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and (resid 335 through 454 or (resid 455 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 456 through 481 or resid 487 through 500 o \ 
r resid 503 through 515))
}

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=0.71 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.060
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
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   0.035   6322  Z= 0.187
  Angle     :  0.660   8.943   8603  Z= 0.367
  Chirality :  0.045   0.212    938
  Planarity :  0.005   0.042   1111
  Dihedral  : 13.270  88.951   2257
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.30 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.99 (0.29), residues: 783
  helix: -3.27 (0.49), residues: 57
  sheet:  0.05 (0.36), residues: 243
  loop : -1.90 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 353 
 HIS   0.001   0.000   HIS O 171 
 PHE   0.014   0.001   PHE C 456 
 TYR   0.017   0.001   TYR C 451 
 ARG   0.007   0.001   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8403 (pmt170) cc_final: 0.8106 (pmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2242
  time to fit residues: 35.2772
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0470
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
A 343 ASN
C 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.179499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.145206 restraints weight = 10825.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.146015 restraints weight = 8229.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.148226 restraints weight = 6372.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3843
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3843 r_free = 0.3843    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3843
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6322  Z= 0.191
  Angle     :  0.613   8.960   8603  Z= 0.322
  Chirality :  0.045   0.156    938
  Planarity :  0.005   0.065   1111
  Dihedral  :  4.372  18.715    870
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.30), residues: 783
  helix: -3.17 (0.54), residues: 53
  sheet:  0.11 (0.35), residues: 243
  loop : -1.64 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.003   0.001   HIS O 171 
 PHE   0.015   0.002   PHE C 456 
 TYR   0.014   0.001   TYR P  54 
 ARG   0.004   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   65 ASP cc_start: 0.7322 (t0) cc_final: 0.7090 (t0)
REVERT: P  150 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6845 (ttpp)
REVERT: O   19 SER cc_start: 0.8107 (m) cc_final: 0.7663 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2128
  time to fit residues: 31.6783
Evaluate side-chains
  91 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 55 optimal weight:    9.9990
   chunk 59 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.4219 r_free = 0.4219 target = 0.179698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.145932 restraints weight = 10871.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.145986 restraints weight = 7955.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.148555 restraints weight = 6376.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6322  Z= 0.187
  Angle     :  0.583   8.584   8603  Z= 0.304
  Chirality :  0.044   0.158    938
  Planarity :  0.005   0.051   1111
  Dihedral  :  4.349  19.367    870
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.30), residues: 783
  helix: -3.07 (0.57), residues: 53
  sheet:  0.27 (0.34), residues: 253
  loop : -1.67 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.003   0.001   HIS P 194 
 PHE   0.017   0.002   PHE A 347 
 TYR   0.013   0.001   TYR A 369 
 ARG   0.004   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  408 ARG cc_start: 0.8421 (pmt170) cc_final: 0.8213 (pmt170)
REVERT: P  150 LYS cc_start: 0.7296 (ttpt) cc_final: 0.7071 (ttpp)
REVERT: O   19 SER cc_start: 0.8016 (m) cc_final: 0.7596 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.2335
  time to fit residues: 36.8935
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0370
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0050
   chunk 14 optimal weight:   20.0000
   chunk 73 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.4472

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.180614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.146109 restraints weight = 10963.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.147290 restraints weight = 8202.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.149780 restraints weight = 6179.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3851 r_free = 0.3851    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3851 r_free = 0.3851    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6322  Z= 0.149
  Angle     :  0.564   8.386   8603  Z= 0.290
  Chirality :  0.044   0.155    938
  Planarity :  0.005   0.061   1111
  Dihedral  :  4.158  17.598    870
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.29), residues: 783
  helix: -3.16 (0.52), residues: 60
  sheet:  0.39 (0.34), residues: 253
  loop : -1.72 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.001   0.001   HIS P 203 
 PHE   0.011   0.001   PHE O  28 
 TYR   0.015   0.001   TYR C 423 
 ARG   0.005   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  150 LYS cc_start: 0.7316 (ttpt) cc_final: 0.7079 (ttpp)
REVERT: O   19 SER cc_start: 0.7965 (m) cc_final: 0.7627 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2183
  time to fit residues: 35.3353
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 55 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0020
   chunk 28 optimal weight:    0.5980
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.0792

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

Flipped N/Q/H residues before XYZ refinement:
O 204 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.176386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.141345 restraints weight = 10879.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.142065 restraints weight = 8159.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.144398 restraints weight = 6308.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3783 r_free = 0.3783    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6322  Z= 0.237
  Angle     :  0.620   8.880   8603  Z= 0.323
  Chirality :  0.046   0.163    938
  Planarity :  0.005   0.056   1111
  Dihedral  :  4.531  19.196    870
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.22 %
    Favored  : 89.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.30), residues: 783
  helix: -2.89 (0.58), residues: 53
  sheet:  0.33 (0.34), residues: 259
  loop : -1.72 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 436 
 HIS   0.003   0.001   HIS O 171 
 PHE   0.020   0.002   PHE A 490 
 TYR   0.016   0.002   TYR P  37 
 ARG   0.005   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.7157 (t80) cc_final: 0.6385 (t80)
REVERT: A  465 GLU cc_start: 0.7142 (tp30) cc_final: 0.6656 (tp30)
REVERT: P  150 LYS cc_start: 0.7368 (ttpt) cc_final: 0.7115 (ttpp)
REVERT: O   19 SER cc_start: 0.8106 (m) cc_final: 0.7653 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2270
  time to fit residues: 37.4266
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0970
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
P 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.179032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.145962 restraints weight = 10867.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.145850 restraints weight = 7823.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148353 restraints weight = 6598.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3849 r_free = 0.3849    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6322  Z= 0.170
  Angle     :  0.594   9.134   8603  Z= 0.304
  Chirality :  0.045   0.158    938
  Planarity :  0.005   0.046   1111
  Dihedral  :  4.298  18.483    870
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.30), residues: 783
  helix: -2.97 (0.57), residues: 53
  sheet:  0.37 (0.34), residues: 259
  loop : -1.66 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.001   0.001   HIS O  32 
 PHE   0.011   0.001   PHE O  28 
 TYR   0.014   0.001   TYR A 369 
 ARG   0.005   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  150 LYS cc_start: 0.7149 (ttpt) cc_final: 0.6904 (ttpp)
REVERT: O   19 SER cc_start: 0.7985 (m) cc_final: 0.7639 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2057
  time to fit residues: 33.2579
Evaluate side-chains
  94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0870
   chunk 63 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
P 171 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.178186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.144866 restraints weight = 10912.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.145763 restraints weight = 7968.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.147394 restraints weight = 6649.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6322  Z= 0.178
  Angle     :  0.590   9.295   8603  Z= 0.302
  Chirality :  0.045   0.156    938
  Planarity :  0.005   0.045   1111
  Dihedral  :  4.237  18.799    870
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.68 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.30), residues: 783
  helix: -3.00 (0.56), residues: 53
  sheet:  0.37 (0.34), residues: 259
  loop : -1.65 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.001   0.001   HIS O 171 
 PHE   0.009   0.001   PHE C 497 
 TYR   0.017   0.001   TYR C 423 
 ARG   0.005   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.7127 (t80) cc_final: 0.6304 (t80)
REVERT: P  127 ASP cc_start: 0.7517 (t0) cc_final: 0.7148 (t0)
REVERT: P  150 LYS cc_start: 0.7140 (ttpt) cc_final: 0.6908 (ttpp)
REVERT: O   19 SER cc_start: 0.8094 (m) cc_final: 0.7641 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2234
  time to fit residues: 34.8746
Evaluate side-chains
  98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0770
   chunk 41 optimal weight:    0.0980
   chunk 18 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
P  36 ASN
O 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.180618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.146733 restraints weight = 10707.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.147785 restraints weight = 8061.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.150046 restraints weight = 5926.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3854
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6322  Z= 0.152
  Angle     :  0.589   8.903   8603  Z= 0.300
  Chirality :  0.044   0.153    938
  Planarity :  0.005   0.048   1111
  Dihedral  :  4.091  19.199    870
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.15 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.44 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.29), residues: 783
  helix: -3.10 (0.52), residues: 60
  sheet:  0.41 (0.33), residues: 259
  loop : -1.72 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 353 
 HIS   0.001   0.001   HIS P 194 
 PHE   0.017   0.001   PHE A 497 
 TYR   0.016   0.001   TYR A 369 
 ARG   0.006   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  478 THR cc_start: 0.6108 (t) cc_final: 0.5313 (t)
REVERT: P  127 ASP cc_start: 0.7497 (t0) cc_final: 0.7156 (t0)
REVERT: P  150 LYS cc_start: 0.7398 (ttpt) cc_final: 0.7110 (ttpp)
REVERT: O   19 SER cc_start: 0.8011 (m) cc_final: 0.7667 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 131
  average time/residue: 0.2054
  time to fit residues: 34.5292
Evaluate side-chains
  102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0370
   chunk 75 optimal weight:    0.0470
   chunk 9 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
P  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.179776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.146498 restraints weight = 10883.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.147240 restraints weight = 7568.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.148965 restraints weight = 6407.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3852 r_free = 0.3852    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6322  Z= 0.165
  Angle     :  0.590   9.021   8603  Z= 0.301
  Chirality :  0.044   0.153    938
  Planarity :  0.005   0.048   1111
  Dihedral  :  4.088  19.178    870
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.05 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.15 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.29), residues: 783
  helix: -3.05 (0.52), residues: 60
  sheet:  0.43 (0.33), residues: 259
  loop : -1.73 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 353 
 HIS   0.001   0.000   HIS O 171 
 PHE   0.015   0.001   PHE A 497 
 TYR   0.016   0.001   TYR A 369 
 ARG   0.007   0.000   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  351 TYR cc_start: 0.6976 (t80) cc_final: 0.6566 (t80)
REVERT: C  478 THR cc_start: 0.6016 (t) cc_final: 0.5237 (t)
REVERT: P  127 ASP cc_start: 0.7644 (t0) cc_final: 0.7267 (t0)
REVERT: P  150 LYS cc_start: 0.7248 (ttpt) cc_final: 0.6995 (ttpp)
REVERT: O   19 SER cc_start: 0.8119 (m) cc_final: 0.7669 (p)
  outliers start: 1
  outliers final: 1
  residues processed: 127
  average time/residue: 0.2030
  time to fit residues: 33.1346
Evaluate side-chains
  104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0870
   overall best weight:    1.1362

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.175320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.141559 restraints weight = 11037.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.141487 restraints weight = 7840.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.143998 restraints weight = 6510.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3782 r_free = 0.3782    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3782 r_free = 0.3782    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6322  Z= 0.247
  Angle     :  0.651   9.500   8603  Z= 0.338
  Chirality :  0.046   0.160    938
  Planarity :  0.005   0.053   1111
  Dihedral  :  4.565  19.052    870
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.60 %
    Favored  : 89.27 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.00 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.29), residues: 783
  helix: -2.94 (0.53), residues: 60
  sheet:  0.34 (0.34), residues: 259
  loop : -1.81 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 353 
 HIS   0.003   0.001   HIS O 171 
 PHE   0.017   0.002   PHE A 497 
 TYR   0.019   0.002   TYR P  37 
 ARG   0.007   0.001   ARG A 466 

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 TYR cc_start: 0.8205 (m-10) cc_final: 0.7950 (m-80)
REVERT: A  465 GLU cc_start: 0.7130 (tp30) cc_final: 0.6640 (tp30)
REVERT: C  478 THR cc_start: 0.6136 (t) cc_final: 0.5318 (t)
REVERT: P  127 ASP cc_start: 0.7507 (t0) cc_final: 0.7122 (t0)
REVERT: P  150 LYS cc_start: 0.7144 (ttpt) cc_final: 0.6890 (ttpp)
  outliers start: 1
  outliers final: 1
  residues processed: 129
  average time/residue: 0.2027
  time to fit residues: 33.5475
Evaluate side-chains
  101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 70 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   overall best weight:    2.2106

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

Flipped N/Q/H residues before XYZ refinement:
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  36 ASN
O 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.169679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.135453 restraints weight = 11143.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.136092 restraints weight = 8851.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.138389 restraints weight = 6699.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.68   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3715 r_free = 0.3715    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.068   6322  Z= 0.428
  Angle     :  0.785  10.402   8603  Z= 0.413
  Chirality :  0.050   0.166    938
  Planarity :  0.006   0.052   1111
  Dihedral  :  5.378  26.101    870
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.49 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  0.44 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.29), residues: 783
  helix: -2.89 (0.58), residues: 53
  sheet: -0.09 (0.33), residues: 258
  loop : -2.01 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 353 
 HIS   0.003   0.001   HIS O 171 
 PHE   0.026   0.003   PHE A 400 
 TYR   0.021   0.003   TYR P  91 
 ARG   0.005   0.001   ARG A 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2323.40 seconds
wall clock time: 41 minutes 1.75 seconds (2461.75 seconds total)