Starting phenix.real_space_refine
on Wed Mar 12 01:59:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uzl_20962/03_2025/6uzl_20962.cif"
  }
  resolution = 4.4
  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=   0.002
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      44      5.16       5
     C    4412      2.51       5
     N    1250      2.21       5
     O    1302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7008
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 3502
          Classifications: {'peptide': 531}
          Incomplete info: {'truncation_to_alanine': 176}
          Link IDs: {'PTRANS': 13, 'TRANS': 517}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 621
          Unresolved non-hydrogen angles: 794
          Unresolved non-hydrogen dihedrals: 486
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 12, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 16, 'ARG:plan': 19}
          Unresolved non-hydrogen planarities: 356
    Chain: "B"
      Number of atoms: 3506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 3506
          Classifications: {'peptide': 531}
          Incomplete info: {'truncation_to_alanine': 175}
          Link IDs: {'PTRANS': 13, 'TRANS': 517}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 617
          Unresolved non-hydrogen angles: 789
          Unresolved non-hydrogen dihedrals: 483
          Unresolved non-hydrogen chiralities: 66
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 12, 'ASP:plan': 14, 'PHE:plan': 5, 'GLU:plan': 15, 'ARG:plan': 19}
          Unresolved non-hydrogen planarities: 352
  Time building chain proxies: 4.80, per 1000 atoms: 0.68
  Number of scatterers: 7008
  At special positions: 0
  Unit cell: (73, 86, 124, 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      44     16.00
     O    1302      8.00
     N    1250      7.00
     C    4412      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: 1.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1988

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 2 sheets defined
      72.8% alpha, 1.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      removed outlier: 3.734A  pdb=" N   LEU A  16 " --> pdb=" O   THR A  12 " (cutoff:3.500A)
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 23 through 54
      removed outlier: 3.700A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ALA A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU A  48 " --> pdb=" O   MET A  44 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LYS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 65 through 111
      removed outlier: 4.281A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.701A  pdb=" N   LYS A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 162
      removed outlier: 4.645A  pdb=" N   ILE A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 193
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 195 through 221
      removed outlier: 3.650A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 5.378A  pdb=" N   LYS A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   GLU A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 268
      removed outlier: 3.891A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 280 through 324
      Proline residue:  A 297  - end of helix
      removed outlier: 4.477A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.256A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 390
      removed outlier: 3.604A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 419
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 458
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.618A  pdb=" N   LYS A 465 " --> pdb=" O   ASP A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 4.015A  pdb=" N   VAL A 479 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 512 through 528
    Processing helix  chain 'B' and resid 12 through 21
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 23 through 54
      removed outlier: 3.864A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 110
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 119
      removed outlier: 3.858A  pdb=" N   GLN B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 162
    Processing helix  chain 'B' and resid 164 through 213
      Proline residue:  B 176  - end of helix
      removed outlier: 3.897A  pdb=" N   GLY B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.760A  pdb=" N   GLU B 226 " --> pdb=" O   GLY B 222 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 280 through 324
      Proline residue:  B 297  - end of helix
      removed outlier: 3.875A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLN B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ARG B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY B 311 " --> pdb=" O   GLN B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
    Processing helix  chain 'B' and resid 401 through 405
      removed outlier: 3.701A  pdb=" N   GLY B 404 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 419
      removed outlier: 3.653A  pdb=" N   ARG B 416 " --> pdb=" O   LEU B 412 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ASN B 417 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 3.686A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASN B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LYS B 465 " --> pdb=" O   ASP B 461 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 459 through 465'
    Processing helix  chain 'B' and resid 474 through 479
      removed outlier: 3.924A  pdb=" N   VAL B 479 " --> pdb=" O   GLU B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 512 through 528
    Processing sheet with id=AA1, first strand: chain 'A' and resid 362 through 366
      removed outlier: 4.932A  pdb=" N   ILE A 362 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 346 " --> pdb=" O   ILE A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503

    568 hydrogen bonds defined for protein.
    1677 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: 1.96

  Time building geometry restraints manager: 2.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2375
        1.34 -     1.46: 1326
        1.46 -     1.58: 3305
        1.58 -     1.70: 0
        1.70 -     1.82: 84
  Bond restraints: 7090
  Sorted by residual:
  bond pdb=" CA  LEU A 374 "
       pdb=" C   LEU A 374 "
    ideal  model  delta    sigma   weight residual
    1.523  1.442  0.081 1.34e-02 5.57e+03 3.64e+01
  bond pdb=" CA  ARG B 360 "
       pdb=" C   ARG B 360 "
    ideal  model  delta    sigma   weight residual
    1.523  1.565 -0.042 1.30e-02 5.92e+03 1.05e+01
  bond pdb=" N   LEU B 359 "
       pdb=" CA  LEU B 359 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.13e+00
  bond pdb=" CA  ALA B 358 "
       pdb=" C   ALA B 358 "
    ideal  model  delta    sigma   weight residual
    1.521  1.556 -0.035 1.20e-02 6.94e+03 8.45e+00
  bond pdb=" CA  PRO B 357 "
       pdb=" C   PRO B 357 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.039 1.42e-02 4.96e+03 7.44e+00
  ... (remaining 7085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.87: 9477
        2.87 -     5.73: 148
        5.73 -     8.60: 31
        8.60 -    11.46: 3
       11.46 -    14.33: 2
  Bond angle restraints: 9661
  Sorted by residual:
  angle pdb=" N   ARG B 360 "
        pdb=" CA  ARG B 360 "
        pdb=" C   ARG B 360 "
      ideal   model   delta    sigma   weight residual
     111.28  125.61  -14.33 1.09e+00 8.42e-01 1.73e+02
  angle pdb=" N   THR B 348 "
        pdb=" CA  THR B 348 "
        pdb=" C   THR B 348 "
      ideal   model   delta    sigma   weight residual
     110.35  121.78  -11.43 1.36e+00 5.41e-01 7.06e+01
  angle pdb=" C   ILE B 366 "
        pdb=" N   PRO B 367 "
        pdb=" CA  PRO B 367 "
      ideal   model   delta    sigma   weight residual
     119.76  127.63   -7.87 1.03e+00 9.43e-01 5.84e+01
  angle pdb=" N   LEU B 364 "
        pdb=" CA  LEU B 364 "
        pdb=" C   LEU B 364 "
      ideal   model   delta    sigma   weight residual
     109.60  119.00   -9.40 1.53e+00 4.27e-01 3.78e+01
  angle pdb=" N   PRO B 352 "
        pdb=" CA  PRO B 352 "
        pdb=" C   PRO B 352 "
      ideal   model   delta    sigma   weight residual
     112.47  100.15   12.32 2.06e+00 2.36e-01 3.58e+01
  ... (remaining 9656 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.92: 3805
       14.92 -    29.84: 338
       29.84 -    44.77: 87
       44.77 -    59.69: 13
       59.69 -    74.61: 6
  Dihedral angle restraints: 4249
    sinusoidal: 1189
      harmonic: 3060
  Sorted by residual:
  dihedral pdb=" CA  TYR B 410 "
           pdb=" C   TYR B 410 "
           pdb=" N   THR B 411 "
           pdb=" CA  THR B 411 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.92  -27.08     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  TYR A 351 "
           pdb=" C   TYR A 351 "
           pdb=" N   PRO A 352 "
           pdb=" CA  PRO A 352 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.58   24.42     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  ARG A 408 "
           pdb=" C   ARG A 408 "
           pdb=" N   GLU A 409 "
           pdb=" CA  GLU A 409 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.34   23.66     0      5.00e+00 4.00e-02 2.24e+01
  ... (remaining 4246 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.086: 1096
       0.086 -    0.171: 104
       0.171 -    0.256: 8
       0.256 -    0.342: 3
       0.342 -    0.427: 1
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" CA  ARG B 360 "
            pdb=" N   ARG B 360 "
            pdb=" C   ARG B 360 "
            pdb=" CB  ARG B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.57e+00
  chirality pdb=" CA  THR B 348 "
            pdb=" N   THR B 348 "
            pdb=" C   THR B 348 "
            pdb=" CB  THR B 348 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.21    0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CA  ILE B 395 "
            pdb=" N   ILE B 395 "
            pdb=" C   ILE B 395 "
            pdb=" CB  ILE B 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.30 2.00e-01 2.50e+01 2.26e+00
  ... (remaining 1209 not shown)

  Planarity restraints: 1249
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 356 "    0.018 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   VAL B 356 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   VAL B 356 "    0.022 2.00e-02 2.50e+03
        pdb=" N   PRO B 357 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 272 "   -0.055 5.00e-02 4.00e+02   8.26e-02 1.09e+01
        pdb=" N   PRO B 273 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO B 273 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 273 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 329 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.76e+00
        pdb=" C   ASP B 329 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ASP B 329 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLU B 330 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1246 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 900
        2.74 -     3.28: 8956
        3.28 -     3.82: 11836
        3.82 -     4.36: 13870
        4.36 -     4.90: 20724
  Nonbonded interactions: 56286
  Sorted by model distance:
  nonbonded pdb=" O   ASN A  37 "
            pdb=" OG  SER A  40 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" O   GLY A 282 "
            pdb=" OG1 THR A 285 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ILE B 128 "
            pdb=" OG  SER B 132 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ALA B 368 "
            pdb=" N   LYS B 370 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   ALA B 314 "
            pdb=" OG1 THR B 317 "
     model   vdw
     2.204 3.040
  ... (remaining 56281 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 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 150 through 541))
}

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 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:             0.680
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.160
  Find NCS groups from input model:        0.220
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   7090  Z= 0.335
  Angle     :  1.004  14.330   9661  Z= 0.657
  Chirality :  0.053   0.427   1212
  Planarity :  0.005   0.083   1249
  Dihedral  : 13.211  74.610   2261
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 27.71
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  : 15.12 %
    Favored  : 84.12 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  8.17 %
    Favored  : 91.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.74 (0.19), residues: 1058
  helix: -2.76 (0.14), residues: 692
  sheet: -2.46 (0.91), residues: 29
  loop : -3.69 (0.27), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  91 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.021   0.002   PHE B 157 
 TYR   0.011   0.002   TYR A  83 
 ARG   0.005   0.001   ARG A 229 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 0.785 
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   75 MET cc_start: 0.9183 (mmm) cc_final: 0.8789 (mmm)
REVERT: A   83 TYR cc_start: 0.8478 (m-10) cc_final: 0.8031 (m-80)
REVERT: A   98 MET cc_start: 0.8924 (mmm) cc_final: 0.8522 (tpp)
REVERT: A  105 PHE cc_start: 0.9279 (m-10) cc_final: 0.8806 (m-80)
REVERT: A  111 MET cc_start: 0.9219 (mmp) cc_final: 0.8914 (mmm)
REVERT: A  156 LEU cc_start: 0.9562 (mt) cc_final: 0.9025 (pp)
REVERT: A  158 ILE cc_start: 0.9469 (mm) cc_final: 0.9264 (mm)
REVERT: A  161 PHE cc_start: 0.8924 (m-10) cc_final: 0.8591 (m-10)
REVERT: A  209 GLN cc_start: 0.9219 (pt0) cc_final: 0.8725 (tm-30)
REVERT: A  228 LYS cc_start: 0.9699 (mttt) cc_final: 0.9320 (mmtm)
REVERT: A  231 ASP cc_start: 0.9302 (m-30) cc_final: 0.9091 (m-30)
REVERT: A  267 LEU cc_start: 0.9493 (mt) cc_final: 0.9287 (mt)
REVERT: A  291 MET cc_start: 0.9079 (mmm) cc_final: 0.8651 (tpt)
REVERT: A  296 ARG cc_start: 0.5657 (mtt180) cc_final: 0.4845 (ttm170)
REVERT: A  303 ASN cc_start: 0.9512 (m-40) cc_final: 0.9244 (p0)
REVERT: A  312 MET cc_start: 0.8752 (mmm) cc_final: 0.8347 (mtt)
REVERT: B   74 LEU cc_start: 0.9685 (mt) cc_final: 0.9440 (mt)
REVERT: B   75 MET cc_start: 0.9407 (mmm) cc_final: 0.8855 (mmm)
REVERT: B   83 TYR cc_start: 0.8427 (m-10) cc_final: 0.8076 (m-80)
REVERT: B   98 MET cc_start: 0.9249 (ttm) cc_final: 0.8957 (ttm)
REVERT: B  105 PHE cc_start: 0.9308 (m-80) cc_final: 0.9005 (m-80)
REVERT: B  131 ASP cc_start: 0.8735 (m-30) cc_final: 0.8425 (m-30)
REVERT: B  159 MET cc_start: 0.8620 (mmp) cc_final: 0.7703 (tpp)
REVERT: B  161 PHE cc_start: 0.8780 (m-10) cc_final: 0.8436 (m-10)
REVERT: B  163 TYR cc_start: 0.8903 (m-10) cc_final: 0.7258 (m-80)
REVERT: B  215 LYS cc_start: 0.9564 (mttt) cc_final: 0.9364 (mmtt)
REVERT: B  228 LYS cc_start: 0.9834 (mttt) cc_final: 0.9403 (mmmm)
REVERT: B  261 LEU cc_start: 0.9463 (mt) cc_final: 0.8966 (tp)
REVERT: B  296 ARG cc_start: 0.5254 (mtt180) cc_final: 0.4607 (ttm-80)
  outliers start: 1
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1802
  time to fit residues: 54.8898
Evaluate side-chains
  188 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:   20.0000
   chunk 83 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   chunk 96 optimal weight:    6.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 191 ASN
A 303 ASN
A 307 GLN
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.080980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.062556 restraints weight = 29198.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.064474 restraints weight = 18939.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.065960 restraints weight = 13617.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7090  Z= 0.240
  Angle     :  0.682   6.797   9661  Z= 0.373
  Chirality :  0.044   0.147   1212
  Planarity :  0.005   0.091   1249
  Dihedral  :  4.852  22.158   1106
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.44 %
    Favored  : 94.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1058
  helix: -0.58 (0.17), residues: 725
  sheet: -1.87 (0.88), residues: 34
  loop : -2.88 (0.33), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  66 
 HIS   0.004   0.001   HIS A 107 
 PHE   0.032   0.002   PHE A 308 
 TYR   0.008   0.001   TYR A  87 
 ARG   0.006   0.001   ARG B  78 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 0.747 
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   41 ASP cc_start: 0.8907 (m-30) cc_final: 0.8676 (m-30)
REVERT: A   75 MET cc_start: 0.9328 (mmm) cc_final: 0.9101 (mmm)
REVERT: A  105 PHE cc_start: 0.9512 (m-10) cc_final: 0.9130 (m-80)
REVERT: A  107 HIS cc_start: 0.8581 (m-70) cc_final: 0.8079 (m170)
REVERT: A  111 MET cc_start: 0.9535 (mmp) cc_final: 0.9040 (mmp)
REVERT: A  133 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9189 (pt0)
REVERT: A  158 ILE cc_start: 0.9430 (mm) cc_final: 0.9149 (mm)
REVERT: A  161 PHE cc_start: 0.8882 (m-10) cc_final: 0.8462 (m-10)
REVERT: A  208 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9202 (tm-30)
REVERT: A  209 GLN cc_start: 0.9072 (pt0) cc_final: 0.8720 (tm-30)
REVERT: A  211 LEU cc_start: 0.9664 (mt) cc_final: 0.9123 (mp)
REVERT: A  224 GLU cc_start: 0.9453 (mp0) cc_final: 0.9044 (mp0)
REVERT: A  228 LYS cc_start: 0.9637 (mttt) cc_final: 0.9297 (mmtm)
REVERT: A  231 ASP cc_start: 0.9367 (m-30) cc_final: 0.8924 (m-30)
REVERT: A  235 ASN cc_start: 0.9498 (m-40) cc_final: 0.8783 (m-40)
REVERT: A  237 MET cc_start: 0.9396 (mmp) cc_final: 0.9132 (mmm)
REVERT: A  242 MET cc_start: 0.9139 (mmm) cc_final: 0.8930 (mmm)
REVERT: A  261 LEU cc_start: 0.9009 (mp) cc_final: 0.8807 (mp)
REVERT: A  288 PHE cc_start: 0.9618 (m-10) cc_final: 0.9397 (m-10)
REVERT: A  291 MET cc_start: 0.9263 (mmm) cc_final: 0.8817 (tpt)
REVERT: A  296 ARG cc_start: 0.5912 (mtt180) cc_final: 0.5418 (ttm170)
REVERT: A  303 ASN cc_start: 0.9684 (m110) cc_final: 0.9102 (p0)
REVERT: A  312 MET cc_start: 0.9059 (mmm) cc_final: 0.8495 (mpp)
REVERT: B   54 ASP cc_start: 0.9349 (m-30) cc_final: 0.8993 (t0)
REVERT: B   67 MET cc_start: 0.9383 (mpp) cc_final: 0.8993 (mpp)
REVERT: B   75 MET cc_start: 0.9598 (mmm) cc_final: 0.8972 (mmm)
REVERT: B   98 MET cc_start: 0.9445 (ttm) cc_final: 0.8870 (ttm)
REVERT: B  105 PHE cc_start: 0.9359 (m-80) cc_final: 0.9058 (m-80)
REVERT: B  121 THR cc_start: 0.9496 (p) cc_final: 0.9245 (t)
REVERT: B  128 ILE cc_start: 0.9427 (mt) cc_final: 0.9156 (mt)
REVERT: B  131 ASP cc_start: 0.8697 (m-30) cc_final: 0.8367 (m-30)
REVERT: B  161 PHE cc_start: 0.8776 (m-10) cc_final: 0.8371 (m-10)
REVERT: B  196 MET cc_start: 0.7901 (tpt) cc_final: 0.7008 (tpp)
REVERT: B  200 MET cc_start: 0.8984 (mtm) cc_final: 0.8564 (mmm)
REVERT: B  215 LYS cc_start: 0.9559 (mttt) cc_final: 0.9279 (mmtt)
REVERT: B  228 LYS cc_start: 0.9814 (mttt) cc_final: 0.9485 (mmmm)
REVERT: B  240 GLN cc_start: 0.8988 (mm-40) cc_final: 0.8730 (tp-100)
REVERT: B  244 MET cc_start: 0.9553 (ttp) cc_final: 0.9253 (ttp)
REVERT: B  261 LEU cc_start: 0.9311 (mt) cc_final: 0.8940 (tp)
REVERT: B  288 PHE cc_start: 0.9572 (m-10) cc_final: 0.9369 (m-80)
REVERT: B  291 MET cc_start: 0.9365 (ttt) cc_final: 0.9089 (ttt)
REVERT: B  295 MET cc_start: 0.9262 (tpt) cc_final: 0.8588 (mmt)
REVERT: B  296 ARG cc_start: 0.5051 (mtt180) cc_final: 0.4617 (ttm170)
REVERT: B  328 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8442 (mmtt)
REVERT: B  329 ASP cc_start: 0.8771 (m-30) cc_final: 0.7958 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1527
  time to fit residues: 51.5883
Evaluate side-chains
  200 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 88 optimal weight:   30.0000
   chunk 40 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 19 optimal weight:    0.3980
   chunk 96 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 33 optimal weight:   50.0000
   chunk 101 optimal weight:   10.0000
   chunk 43 optimal weight:    9.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.079662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.060652 restraints weight = 30652.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.062595 restraints weight = 20021.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.064035 restraints weight = 14445.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7090  Z= 0.264
  Angle     :  0.667   6.791   9661  Z= 0.364
  Chirality :  0.044   0.190   1212
  Planarity :  0.005   0.088   1249
  Dihedral  :  4.597  22.742   1106
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.45 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.88 (0.25), residues: 1058
  helix:  0.32 (0.19), residues: 728
  sheet: -1.32 (1.00), residues: 24
  loop : -2.69 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  66 
 HIS   0.005   0.002   HIS B 214 
 PHE   0.020   0.002   PHE B 308 
 TYR   0.012   0.001   TYR B  83 
 ARG   0.003   0.000   ARG B  78 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 223
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASN cc_start: 0.9140 (t0) cc_final: 0.8768 (t0)
REVERT: A   47 LEU cc_start: 0.9566 (mt) cc_final: 0.9351 (mt)
REVERT: A   75 MET cc_start: 0.9312 (mmm) cc_final: 0.9001 (mmm)
REVERT: A   83 TYR cc_start: 0.7506 (t80) cc_final: 0.7301 (t80)
REVERT: A  105 PHE cc_start: 0.9473 (m-80) cc_final: 0.9094 (m-80)
REVERT: A  107 HIS cc_start: 0.8712 (m-70) cc_final: 0.8380 (m170)
REVERT: A  131 ASP cc_start: 0.8695 (m-30) cc_final: 0.8390 (m-30)
REVERT: A  133 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9146 (mt-10)
REVERT: A  158 ILE cc_start: 0.9394 (mm) cc_final: 0.9097 (mm)
REVERT: A  161 PHE cc_start: 0.8871 (m-10) cc_final: 0.8438 (m-10)
REVERT: A  208 GLU cc_start: 0.9435 (tm-30) cc_final: 0.9215 (tm-30)
REVERT: A  209 GLN cc_start: 0.9174 (pt0) cc_final: 0.8933 (tm-30)
REVERT: A  211 LEU cc_start: 0.9655 (mt) cc_final: 0.9291 (mt)
REVERT: A  214 HIS cc_start: 0.8205 (m90) cc_final: 0.7130 (m-70)
REVERT: A  224 GLU cc_start: 0.9432 (mp0) cc_final: 0.9086 (mp0)
REVERT: A  228 LYS cc_start: 0.9685 (mttt) cc_final: 0.9320 (mmtm)
REVERT: A  231 ASP cc_start: 0.9366 (m-30) cc_final: 0.8896 (m-30)
REVERT: A  235 ASN cc_start: 0.9520 (m-40) cc_final: 0.8750 (m-40)
REVERT: A  288 PHE cc_start: 0.9577 (m-10) cc_final: 0.9334 (m-10)
REVERT: A  291 MET cc_start: 0.9188 (mmm) cc_final: 0.8676 (tpt)
REVERT: A  303 ASN cc_start: 0.9616 (m110) cc_final: 0.9221 (p0)
REVERT: A  312 MET cc_start: 0.8967 (mmm) cc_final: 0.8357 (mtt)
REVERT: B   75 MET cc_start: 0.9585 (mmm) cc_final: 0.9376 (mmm)
REVERT: B   98 MET cc_start: 0.9408 (ttm) cc_final: 0.8938 (ttm)
REVERT: B  105 PHE cc_start: 0.9433 (m-80) cc_final: 0.8988 (m-80)
REVERT: B  121 THR cc_start: 0.9489 (p) cc_final: 0.9228 (t)
REVERT: B  131 ASP cc_start: 0.8667 (m-30) cc_final: 0.8444 (m-30)
REVERT: B  161 PHE cc_start: 0.8793 (m-10) cc_final: 0.8324 (m-10)
REVERT: B  200 MET cc_start: 0.8987 (mtm) cc_final: 0.8563 (mmm)
REVERT: B  208 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8868 (tm-30)
REVERT: B  215 LYS cc_start: 0.9516 (mttt) cc_final: 0.9276 (mmmt)
REVERT: B  242 MET cc_start: 0.9291 (mpp) cc_final: 0.8910 (mmt)
REVERT: B  244 MET cc_start: 0.9483 (ttp) cc_final: 0.9207 (ttp)
REVERT: B  261 LEU cc_start: 0.9358 (mt) cc_final: 0.8914 (tp)
REVERT: B  288 PHE cc_start: 0.9528 (m-10) cc_final: 0.9300 (m-10)
REVERT: B  296 ARG cc_start: 0.5397 (mtt180) cc_final: 0.4665 (ttm170)
REVERT: B  312 MET cc_start: 0.9243 (mmm) cc_final: 0.8881 (mmm)
REVERT: B  325 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8997 (mt-10)
REVERT: B  328 LYS cc_start: 0.8994 (mmtm) cc_final: 0.8519 (mmtt)
REVERT: B  329 ASP cc_start: 0.8725 (m-30) cc_final: 0.8004 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 223
  average time/residue: 0.1573
  time to fit residues: 48.7345
Evaluate side-chains
  184 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   chunk 29 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 50 optimal weight:    8.9990
   chunk 35 optimal weight:   30.0000
   chunk 39 optimal weight:    7.9990
   chunk 99 optimal weight:   30.0000
   chunk 60 optimal weight:    0.5980
   chunk 6 optimal weight:    4.9990
   overall best weight:    2.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 191 ASN
A 198 ASN
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 ASN
B 209 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.077824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.059943 restraints weight = 30371.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.061840 restraints weight = 19751.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.063296 restraints weight = 14271.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.4346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7090  Z= 0.258
  Angle     :  0.654   6.816   9661  Z= 0.357
  Chirality :  0.044   0.148   1212
  Planarity :  0.005   0.088   1249
  Dihedral  :  4.432  21.091   1106
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.63 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.28 (0.26), residues: 1058
  helix:  0.77 (0.19), residues: 730
  sheet: -1.62 (0.97), residues: 24
  loop : -2.41 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A  66 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.022   0.002   PHE B 308 
 TYR   0.011   0.001   TYR A  83 
 ARG   0.004   0.000   ARG B 148 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 219
  time to evaluate  : 0.777 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.9027 (mtt180) cc_final: 0.8798 (mtm-85)
REVERT: A   37 ASN cc_start: 0.9131 (t0) cc_final: 0.8818 (t0)
REVERT: A   47 LEU cc_start: 0.9584 (mt) cc_final: 0.9339 (mt)
REVERT: A   53 ASP cc_start: 0.8788 (m-30) cc_final: 0.8577 (m-30)
REVERT: A   75 MET cc_start: 0.9340 (mmm) cc_final: 0.9042 (mmm)
REVERT: A   83 TYR cc_start: 0.7844 (t80) cc_final: 0.7643 (t80)
REVERT: A  105 PHE cc_start: 0.9496 (m-80) cc_final: 0.9088 (m-80)
REVERT: A  107 HIS cc_start: 0.8598 (m-70) cc_final: 0.8293 (m170)
REVERT: A  131 ASP cc_start: 0.8736 (m-30) cc_final: 0.8491 (m-30)
REVERT: A  133 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9133 (mt-10)
REVERT: A  161 PHE cc_start: 0.8848 (m-10) cc_final: 0.8541 (m-10)
REVERT: A  209 GLN cc_start: 0.9165 (pt0) cc_final: 0.8953 (pp30)
REVERT: A  211 LEU cc_start: 0.9723 (mt) cc_final: 0.9265 (mt)
REVERT: A  214 HIS cc_start: 0.7705 (m90) cc_final: 0.7240 (m170)
REVERT: A  244 MET cc_start: 0.9384 (mtt) cc_final: 0.9160 (mtt)
REVERT: A  288 PHE cc_start: 0.9623 (m-10) cc_final: 0.9383 (m-10)
REVERT: A  291 MET cc_start: 0.9255 (mmm) cc_final: 0.8754 (tpt)
REVERT: A  303 ASN cc_start: 0.9618 (m110) cc_final: 0.9236 (p0)
REVERT: A  312 MET cc_start: 0.9031 (mmm) cc_final: 0.8456 (mtt)
REVERT: B   54 ASP cc_start: 0.9359 (m-30) cc_final: 0.8972 (t0)
REVERT: B   66 TRP cc_start: 0.7599 (t60) cc_final: 0.7392 (t60)
REVERT: B   67 MET cc_start: 0.9361 (mpp) cc_final: 0.9152 (mpp)
REVERT: B   75 MET cc_start: 0.9608 (mmm) cc_final: 0.9395 (mmm)
REVERT: B   98 MET cc_start: 0.9377 (ttm) cc_final: 0.9155 (ttm)
REVERT: B  105 PHE cc_start: 0.9482 (m-10) cc_final: 0.9048 (m-80)
REVERT: B  121 THR cc_start: 0.9491 (p) cc_final: 0.9225 (t)
REVERT: B  131 ASP cc_start: 0.8667 (m-30) cc_final: 0.8442 (m-30)
REVERT: B  161 PHE cc_start: 0.8773 (m-10) cc_final: 0.8313 (m-10)
REVERT: B  196 MET cc_start: 0.6725 (tpp) cc_final: 0.6504 (tpp)
REVERT: B  200 MET cc_start: 0.9046 (mtm) cc_final: 0.8728 (mmm)
REVERT: B  211 LEU cc_start: 0.9841 (mt) cc_final: 0.9557 (mt)
REVERT: B  242 MET cc_start: 0.9300 (mpp) cc_final: 0.8852 (mmt)
REVERT: B  288 PHE cc_start: 0.9548 (m-10) cc_final: 0.9334 (m-10)
REVERT: B  296 ARG cc_start: 0.5163 (mtt180) cc_final: 0.4674 (ttm170)
REVERT: B  325 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8989 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 219
  average time/residue: 0.1660
  time to fit residues: 51.0705
Evaluate side-chains
  180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 89 optimal weight:   50.0000
   chunk 69 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0270
   chunk 87 optimal weight:    8.9990
   chunk 53 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 41 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    1.7444

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.080310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.061455 restraints weight = 30260.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.063310 restraints weight = 20368.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.064704 restraints weight = 14996.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.4761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7090  Z= 0.209
  Angle     :  0.628   6.935   9661  Z= 0.340
  Chirality :  0.043   0.148   1212
  Planarity :  0.005   0.089   1249
  Dihedral  :  4.326  21.579   1106
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  3.27 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.13 (0.26), residues: 1058
  helix:  1.11 (0.19), residues: 733
  sheet: -1.68 (0.98), residues: 24
  loop : -2.34 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  91 
 HIS   0.007   0.002   HIS A 214 
 PHE   0.013   0.002   PHE B 308 
 TYR   0.008   0.001   TYR A 163 
 ARG   0.003   0.000   ARG A 190 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 212
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASN cc_start: 0.8885 (t0) cc_final: 0.8625 (t0)
REVERT: A   47 LEU cc_start: 0.9548 (mt) cc_final: 0.9270 (mt)
REVERT: A   75 MET cc_start: 0.9313 (mmm) cc_final: 0.9001 (mmm)
REVERT: A  105 PHE cc_start: 0.9506 (m-80) cc_final: 0.8996 (m-80)
REVERT: A  107 HIS cc_start: 0.8637 (m-70) cc_final: 0.8253 (m170)
REVERT: A  131 ASP cc_start: 0.8675 (m-30) cc_final: 0.8424 (m-30)
REVERT: A  133 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9073 (pt0)
REVERT: A  159 MET cc_start: 0.9026 (tpp) cc_final: 0.8728 (tpp)
REVERT: A  161 PHE cc_start: 0.8811 (m-10) cc_final: 0.8478 (m-10)
REVERT: A  231 ASP cc_start: 0.9283 (m-30) cc_final: 0.9074 (m-30)
REVERT: A  288 PHE cc_start: 0.9549 (m-10) cc_final: 0.9346 (m-10)
REVERT: A  291 MET cc_start: 0.9168 (mmm) cc_final: 0.8675 (tpt)
REVERT: A  303 ASN cc_start: 0.9573 (m110) cc_final: 0.9195 (p0)
REVERT: A  312 MET cc_start: 0.9080 (mmm) cc_final: 0.8348 (mtt)
REVERT: B   54 ASP cc_start: 0.9324 (m-30) cc_final: 0.8890 (t0)
REVERT: B   66 TRP cc_start: 0.7496 (t60) cc_final: 0.7167 (t60)
REVERT: B   67 MET cc_start: 0.9330 (mpp) cc_final: 0.9006 (mpp)
REVERT: B   75 MET cc_start: 0.9571 (mmm) cc_final: 0.9336 (mmm)
REVERT: B   98 MET cc_start: 0.9382 (ttm) cc_final: 0.9178 (ttm)
REVERT: B  105 PHE cc_start: 0.9474 (m-10) cc_final: 0.9059 (m-80)
REVERT: B  108 MET cc_start: 0.9048 (mtm) cc_final: 0.8835 (mtt)
REVERT: B  121 THR cc_start: 0.9450 (p) cc_final: 0.9162 (t)
REVERT: B  131 ASP cc_start: 0.8568 (m-30) cc_final: 0.8171 (m-30)
REVERT: B  160 MET cc_start: 0.9298 (ptp) cc_final: 0.9070 (ptp)
REVERT: B  161 PHE cc_start: 0.8740 (m-10) cc_final: 0.8251 (m-10)
REVERT: B  196 MET cc_start: 0.6719 (tpp) cc_final: 0.6476 (tpp)
REVERT: B  200 MET cc_start: 0.9009 (mtm) cc_final: 0.8737 (mmm)
REVERT: B  211 LEU cc_start: 0.9826 (mt) cc_final: 0.9550 (mt)
REVERT: B  231 ASP cc_start: 0.9493 (m-30) cc_final: 0.9237 (m-30)
REVERT: B  242 MET cc_start: 0.9225 (mpp) cc_final: 0.8825 (mmt)
REVERT: B  288 PHE cc_start: 0.9508 (m-10) cc_final: 0.9292 (m-10)
REVERT: B  296 ARG cc_start: 0.5253 (mtt180) cc_final: 0.4650 (ttp-170)
  outliers start: 2
  outliers final: 1
  residues processed: 213
  average time/residue: 0.1353
  time to fit residues: 41.2487
Evaluate side-chains
  186 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 44 optimal weight:    6.9990
   chunk 98 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 89 optimal weight:   50.0000
   chunk 26 optimal weight:   20.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.077667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.059363 restraints weight = 31117.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.061177 restraints weight = 20508.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.062542 restraints weight = 14902.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.4978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7090  Z= 0.280
  Angle     :  0.668   6.977   9661  Z= 0.369
  Chirality :  0.044   0.153   1212
  Planarity :  0.005   0.084   1249
  Dihedral  :  4.480  23.888   1106
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.03 (0.26), residues: 1058
  helix:  0.96 (0.19), residues: 737
  sheet: -1.68 (1.02), residues: 24
  loop : -2.37 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  66 
 HIS   0.008   0.002   HIS A 214 
 PHE   0.026   0.002   PHE A 308 
 TYR   0.007   0.001   TYR A  87 
 ARG   0.003   0.000   ARG B 148 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASN cc_start: 0.8962 (t0) cc_final: 0.8721 (t0)
REVERT: A   47 LEU cc_start: 0.9537 (mt) cc_final: 0.9279 (mt)
REVERT: A   75 MET cc_start: 0.9334 (mmm) cc_final: 0.9023 (mmm)
REVERT: A  105 PHE cc_start: 0.9462 (m-80) cc_final: 0.9023 (m-80)
REVERT: A  107 HIS cc_start: 0.8589 (m-70) cc_final: 0.8238 (m170)
REVERT: A  131 ASP cc_start: 0.8740 (m-30) cc_final: 0.8515 (m-30)
REVERT: A  133 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9117 (mt-10)
REVERT: A  158 ILE cc_start: 0.9335 (mm) cc_final: 0.9092 (mm)
REVERT: A  161 PHE cc_start: 0.8814 (m-10) cc_final: 0.8376 (m-10)
REVERT: A  242 MET cc_start: 0.9325 (mmp) cc_final: 0.9110 (mmm)
REVERT: A  288 PHE cc_start: 0.9577 (m-10) cc_final: 0.9339 (m-10)
REVERT: A  291 MET cc_start: 0.9252 (mmm) cc_final: 0.8821 (tpt)
REVERT: A  303 ASN cc_start: 0.9609 (m110) cc_final: 0.9181 (p0)
REVERT: A  312 MET cc_start: 0.9086 (mmm) cc_final: 0.8341 (mtt)
REVERT: B   67 MET cc_start: 0.9415 (mpp) cc_final: 0.9188 (mpp)
REVERT: B   75 MET cc_start: 0.9624 (mmm) cc_final: 0.9404 (mmm)
REVERT: B  105 PHE cc_start: 0.9380 (m-80) cc_final: 0.8978 (m-80)
REVERT: B  108 MET cc_start: 0.9170 (mtm) cc_final: 0.8958 (mtt)
REVERT: B  131 ASP cc_start: 0.8665 (m-30) cc_final: 0.8436 (m-30)
REVERT: B  161 PHE cc_start: 0.8831 (m-10) cc_final: 0.8347 (m-10)
REVERT: B  196 MET cc_start: 0.6906 (tpp) cc_final: 0.6575 (tpp)
REVERT: B  200 MET cc_start: 0.9005 (mtm) cc_final: 0.8737 (mmm)
REVERT: B  242 MET cc_start: 0.9196 (mpp) cc_final: 0.8804 (mmt)
REVERT: B  288 PHE cc_start: 0.9540 (m-10) cc_final: 0.9333 (m-10)
REVERT: B  296 ARG cc_start: 0.4936 (mtt180) cc_final: 0.4532 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.1373
  time to fit residues: 41.6842
Evaluate side-chains
  177 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 45 optimal weight:   30.0000
   chunk 87 optimal weight:    0.9980
   chunk 95 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 17 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 32 optimal weight:    0.3980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.080013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.061041 restraints weight = 29691.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062972 restraints weight = 19686.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.064426 restraints weight = 14352.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7090  Z= 0.197
  Angle     :  0.638   6.868   9661  Z= 0.342
  Chirality :  0.043   0.152   1212
  Planarity :  0.005   0.086   1249
  Dihedral  :  4.279  21.834   1106
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.27), residues: 1058
  helix:  1.33 (0.19), residues: 733
  sheet: -1.57 (1.06), residues: 24
  loop : -2.15 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  91 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.034   0.002   PHE B  43 
 TYR   0.009   0.001   TYR A 163 
 ARG   0.002   0.000   ARG B  78 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.9539 (mt) cc_final: 0.9239 (mt)
REVERT: A   53 ASP cc_start: 0.8788 (m-30) cc_final: 0.8587 (m-30)
REVERT: A   75 MET cc_start: 0.9357 (mmm) cc_final: 0.9065 (mmm)
REVERT: A  105 PHE cc_start: 0.9506 (m-80) cc_final: 0.9017 (m-80)
REVERT: A  107 HIS cc_start: 0.8595 (m-70) cc_final: 0.8271 (m170)
REVERT: A  127 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8712 (tpp-160)
REVERT: A  133 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9076 (mt-10)
REVERT: A  161 PHE cc_start: 0.8806 (m-10) cc_final: 0.8372 (m-10)
REVERT: A  210 MET cc_start: 0.9160 (tmm) cc_final: 0.8735 (tmm)
REVERT: A  211 LEU cc_start: 0.9736 (mt) cc_final: 0.9519 (mt)
REVERT: A  231 ASP cc_start: 0.9323 (m-30) cc_final: 0.8730 (m-30)
REVERT: A  235 ASN cc_start: 0.9501 (m-40) cc_final: 0.8576 (m-40)
REVERT: A  291 MET cc_start: 0.9198 (mmm) cc_final: 0.8802 (tpt)
REVERT: A  303 ASN cc_start: 0.9607 (m110) cc_final: 0.9141 (p0)
REVERT: A  312 MET cc_start: 0.9094 (mmm) cc_final: 0.8406 (mtt)
REVERT: B   43 PHE cc_start: 0.9055 (m-80) cc_final: 0.8854 (m-80)
REVERT: B   54 ASP cc_start: 0.9554 (m-30) cc_final: 0.9021 (t0)
REVERT: B   75 MET cc_start: 0.9584 (mmm) cc_final: 0.9176 (mmm)
REVERT: B   98 MET cc_start: 0.9373 (ttt) cc_final: 0.7972 (ttt)
REVERT: B  102 ARG cc_start: 0.9226 (ttm170) cc_final: 0.8618 (mtt-85)
REVERT: B  105 PHE cc_start: 0.9445 (m-80) cc_final: 0.9136 (m-80)
REVERT: B  121 THR cc_start: 0.9446 (p) cc_final: 0.9115 (t)
REVERT: B  127 ARG cc_start: 0.9235 (tpp80) cc_final: 0.8891 (tpp-160)
REVERT: B  160 MET cc_start: 0.9350 (ptp) cc_final: 0.9108 (ptp)
REVERT: B  161 PHE cc_start: 0.8781 (m-10) cc_final: 0.8287 (m-10)
REVERT: B  196 MET cc_start: 0.6802 (tpp) cc_final: 0.6575 (tpp)
REVERT: B  200 MET cc_start: 0.8938 (mtm) cc_final: 0.8696 (mmm)
REVERT: B  231 ASP cc_start: 0.9492 (m-30) cc_final: 0.9172 (m-30)
REVERT: B  242 MET cc_start: 0.9240 (mpp) cc_final: 0.8867 (mmt)
REVERT: B  288 PHE cc_start: 0.9523 (m-10) cc_final: 0.9316 (m-10)
REVERT: B  295 MET cc_start: 0.9234 (tpt) cc_final: 0.8430 (mmt)
REVERT: B  296 ARG cc_start: 0.5083 (mtt180) cc_final: 0.4732 (ttm170)
REVERT: B  312 MET cc_start: 0.9218 (mmm) cc_final: 0.8826 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.1547
  time to fit residues: 49.0063
Evaluate side-chains
  196 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 102 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 88 optimal weight:   30.0000
   overall best weight:    1.2784

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.079688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.061758 restraints weight = 29794.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.063622 restraints weight = 20018.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.065099 restraints weight = 14741.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7090  Z= 0.198
  Angle     :  0.646   6.673   9661  Z= 0.349
  Chirality :  0.044   0.156   1212
  Planarity :  0.005   0.086   1249
  Dihedral  :  4.226  23.211   1106
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.53 (0.27), residues: 1058
  helix:  1.35 (0.19), residues: 738
  sheet: -1.60 (1.08), residues: 24
  loop : -2.05 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  91 
 HIS   0.002   0.001   HIS A 214 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.008   0.001   TYR A 163 
 ARG   0.002   0.000   ARG A 238 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.9521 (mt) cc_final: 0.9228 (mt)
REVERT: A   75 MET cc_start: 0.9318 (mmm) cc_final: 0.9006 (mmm)
REVERT: A  105 PHE cc_start: 0.9461 (m-80) cc_final: 0.8982 (m-80)
REVERT: A  107 HIS cc_start: 0.8655 (m-70) cc_final: 0.8302 (m170)
REVERT: A  131 ASP cc_start: 0.8638 (m-30) cc_final: 0.8417 (m-30)
REVERT: A  133 GLU cc_start: 0.9424 (mt-10) cc_final: 0.9062 (mt-10)
REVERT: A  161 PHE cc_start: 0.8708 (m-10) cc_final: 0.8276 (m-10)
REVERT: A  210 MET cc_start: 0.9161 (tmm) cc_final: 0.8779 (tmm)
REVERT: A  211 LEU cc_start: 0.9713 (mt) cc_final: 0.9369 (mt)
REVERT: A  231 ASP cc_start: 0.9268 (m-30) cc_final: 0.8970 (m-30)
REVERT: A  242 MET cc_start: 0.9318 (mmp) cc_final: 0.9099 (mmm)
REVERT: A  252 ASP cc_start: 0.8382 (t0) cc_final: 0.8174 (t0)
REVERT: A  288 PHE cc_start: 0.9521 (m-10) cc_final: 0.9315 (m-10)
REVERT: A  291 MET cc_start: 0.9177 (mmm) cc_final: 0.8804 (tpt)
REVERT: A  304 VAL cc_start: 0.8822 (t) cc_final: 0.8497 (t)
REVERT: B   54 ASP cc_start: 0.9558 (m-30) cc_final: 0.9018 (t0)
REVERT: B   75 MET cc_start: 0.9516 (mmm) cc_final: 0.9084 (mmm)
REVERT: B   98 MET cc_start: 0.9413 (ttt) cc_final: 0.8167 (ttt)
REVERT: B  102 ARG cc_start: 0.9152 (ttm170) cc_final: 0.8518 (mtt-85)
REVERT: B  105 PHE cc_start: 0.9343 (m-80) cc_final: 0.9023 (m-80)
REVERT: B  121 THR cc_start: 0.9410 (p) cc_final: 0.9039 (t)
REVERT: B  127 ARG cc_start: 0.9166 (tpp80) cc_final: 0.8881 (tpp-160)
REVERT: B  131 ASP cc_start: 0.8690 (m-30) cc_final: 0.8489 (m-30)
REVERT: B  160 MET cc_start: 0.9273 (ptp) cc_final: 0.9039 (ptp)
REVERT: B  161 PHE cc_start: 0.8794 (m-10) cc_final: 0.8324 (m-10)
REVERT: B  196 MET cc_start: 0.6845 (tpp) cc_final: 0.6605 (tpp)
REVERT: B  242 MET cc_start: 0.9255 (mpp) cc_final: 0.8857 (mmt)
REVERT: B  244 MET cc_start: 0.9489 (ttp) cc_final: 0.9282 (ttp)
REVERT: B  288 PHE cc_start: 0.9504 (m-10) cc_final: 0.9277 (m-10)
REVERT: B  296 ARG cc_start: 0.5308 (mtt180) cc_final: 0.4993 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.1445
  time to fit residues: 43.9791
Evaluate side-chains
  185 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 86 optimal weight:   50.0000
   chunk 100 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 41 optimal weight:   40.0000
   chunk 45 optimal weight:   40.0000
   chunk 80 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.078578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.060957 restraints weight = 30844.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.062859 restraints weight = 20583.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.064300 restraints weight = 15017.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.5828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7090  Z= 0.244
  Angle     :  0.693   7.165   9661  Z= 0.376
  Chirality :  0.044   0.197   1212
  Planarity :  0.005   0.082   1249
  Dihedral  :  4.243  22.029   1106
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.37 (0.27), residues: 1058
  helix:  1.18 (0.19), residues: 741
  sheet: -1.55 (1.13), residues: 24
  loop : -2.04 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  91 
 HIS   0.003   0.001   HIS A 107 
 PHE   0.022   0.002   PHE A 308 
 TYR   0.008   0.001   TYR A 162 
 ARG   0.003   0.000   ARG B 310 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.8921 (m-80) cc_final: 0.8398 (m-80)
REVERT: A   47 LEU cc_start: 0.9515 (mt) cc_final: 0.9221 (mt)
REVERT: A   53 ASP cc_start: 0.8800 (m-30) cc_final: 0.8581 (m-30)
REVERT: A   75 MET cc_start: 0.9362 (mmm) cc_final: 0.9057 (mmm)
REVERT: A  105 PHE cc_start: 0.9476 (m-80) cc_final: 0.9001 (m-80)
REVERT: A  107 HIS cc_start: 0.8616 (m-70) cc_final: 0.8269 (m170)
REVERT: A  131 ASP cc_start: 0.8692 (m-30) cc_final: 0.8423 (m-30)
REVERT: A  133 GLU cc_start: 0.9438 (mt-10) cc_final: 0.9089 (mt-10)
REVERT: A  161 PHE cc_start: 0.8674 (m-10) cc_final: 0.8206 (m-10)
REVERT: A  210 MET cc_start: 0.9193 (tmm) cc_final: 0.8903 (tmm)
REVERT: A  288 PHE cc_start: 0.9545 (m-10) cc_final: 0.9330 (m-10)
REVERT: A  291 MET cc_start: 0.9214 (mmm) cc_final: 0.8803 (tpt)
REVERT: A  304 VAL cc_start: 0.8838 (t) cc_final: 0.8529 (t)
REVERT: A  312 MET cc_start: 0.8989 (mmm) cc_final: 0.8201 (mtt)
REVERT: B   54 ASP cc_start: 0.9577 (m-30) cc_final: 0.9109 (t0)
REVERT: B   75 MET cc_start: 0.9544 (mmm) cc_final: 0.9148 (mmm)
REVERT: B  105 PHE cc_start: 0.9378 (m-80) cc_final: 0.9009 (m-80)
REVERT: B  116 PHE cc_start: 0.7741 (m-10) cc_final: 0.7533 (m-10)
REVERT: B  127 ARG cc_start: 0.9185 (tpp80) cc_final: 0.8884 (tpp-160)
REVERT: B  131 ASP cc_start: 0.8713 (m-30) cc_final: 0.8511 (m-30)
REVERT: B  161 PHE cc_start: 0.8829 (m-10) cc_final: 0.8377 (m-10)
REVERT: B  200 MET cc_start: 0.8641 (mpp) cc_final: 0.8347 (mpp)
REVERT: B  242 MET cc_start: 0.9212 (mpp) cc_final: 0.8788 (mmt)
REVERT: B  296 ARG cc_start: 0.5443 (mtt180) cc_final: 0.5006 (ttm170)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.1460
  time to fit residues: 43.9129
Evaluate side-chains
  180 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 101 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 86 optimal weight:   50.0000
   chunk 69 optimal weight:    0.8980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.081699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062551 restraints weight = 30395.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.064519 restraints weight = 20541.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.066016 restraints weight = 15131.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.6112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7090  Z= 0.206
  Angle     :  0.684   8.097   9661  Z= 0.364
  Chirality :  0.044   0.165   1212
  Planarity :  0.005   0.082   1249
  Dihedral  :  4.147  21.346   1106
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.54 (0.27), residues: 1058
  helix:  1.27 (0.19), residues: 737
  sheet: -1.04 (1.07), residues: 29
  loop : -1.83 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  91 
 HIS   0.007   0.002   HIS A 214 
 PHE   0.023   0.002   PHE A 308 
 TYR   0.007   0.001   TYR B 162 
 ARG   0.002   0.000   ARG A 127 

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

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

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2116 Ramachandran restraints generated.
    1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.806 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.9511 (mt) cc_final: 0.9200 (mt)
REVERT: A   75 MET cc_start: 0.9330 (mmm) cc_final: 0.9018 (mmm)
REVERT: A   98 MET cc_start: 0.9173 (tpp) cc_final: 0.8821 (tpp)
REVERT: A  105 PHE cc_start: 0.9479 (m-80) cc_final: 0.8998 (m-80)
REVERT: A  107 HIS cc_start: 0.8635 (m-70) cc_final: 0.8316 (m170)
REVERT: A  127 ARG cc_start: 0.9096 (tpp80) cc_final: 0.8858 (tpp80)
REVERT: A  133 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9090 (pt0)
REVERT: A  159 MET cc_start: 0.9355 (tpp) cc_final: 0.9138 (tpp)
REVERT: A  161 PHE cc_start: 0.8676 (m-10) cc_final: 0.8246 (m-10)
REVERT: A  180 ILE cc_start: 0.9157 (tt) cc_final: 0.8930 (pt)
REVERT: A  211 LEU cc_start: 0.9723 (mt) cc_final: 0.9441 (mt)
REVERT: A  231 ASP cc_start: 0.9274 (m-30) cc_final: 0.8764 (m-30)
REVERT: A  235 ASN cc_start: 0.9596 (m-40) cc_final: 0.9177 (m-40)
REVERT: A  242 MET cc_start: 0.9362 (mmp) cc_final: 0.9068 (mmm)
REVERT: A  288 PHE cc_start: 0.9500 (m-10) cc_final: 0.9291 (m-10)
REVERT: A  291 MET cc_start: 0.9179 (mmm) cc_final: 0.8817 (tpt)
REVERT: A  312 MET cc_start: 0.9007 (mmm) cc_final: 0.8114 (mtt)
REVERT: B   54 ASP cc_start: 0.9555 (m-30) cc_final: 0.9017 (t0)
REVERT: B   75 MET cc_start: 0.9496 (mmm) cc_final: 0.9038 (mmm)
REVERT: B   98 MET cc_start: 0.9382 (ttt) cc_final: 0.8498 (ttt)
REVERT: B  102 ARG cc_start: 0.9133 (ttm170) cc_final: 0.8640 (ttm170)
REVERT: B  105 PHE cc_start: 0.9429 (m-80) cc_final: 0.9060 (m-80)
REVERT: B  127 ARG cc_start: 0.9145 (tpp80) cc_final: 0.8858 (tpp-160)
REVERT: B  131 ASP cc_start: 0.8672 (m-30) cc_final: 0.8455 (m-30)
REVERT: B  156 LEU cc_start: 0.9567 (mt) cc_final: 0.9215 (pp)
REVERT: B  161 PHE cc_start: 0.8743 (m-10) cc_final: 0.8292 (m-10)
REVERT: B  231 ASP cc_start: 0.9426 (m-30) cc_final: 0.9074 (m-30)
REVERT: B  242 MET cc_start: 0.9189 (mpp) cc_final: 0.8693 (mmt)
REVERT: B  288 PHE cc_start: 0.9510 (m-10) cc_final: 0.9250 (m-10)
REVERT: B  294 LEU cc_start: 0.9566 (mt) cc_final: 0.9260 (mt)
REVERT: B  296 ARG cc_start: 0.5455 (mtt180) cc_final: 0.5101 (ttm170)
REVERT: B  312 MET cc_start: 0.9109 (mmm) cc_final: 0.8831 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1492
  time to fit residues: 45.2399
Evaluate side-chains
  196 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0370
   chunk 66 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 69 optimal weight:    0.0770
   chunk 94 optimal weight:   30.0000
   chunk 74 optimal weight:    0.0670
   chunk 19 optimal weight:    8.9990
   chunk 45 optimal weight:   30.0000
   chunk 25 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.3154

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.083916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.064615 restraints weight = 29217.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.066636 restraints weight = 19978.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.068191 restraints weight = 14770.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.6564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7090  Z= 0.190
  Angle     :  0.692  11.828   9661  Z= 0.362
  Chirality :  0.044   0.163   1212
  Planarity :  0.005   0.080   1249
  Dihedral  :  3.998  20.988   1106
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.63 (0.27), residues: 1058
  helix:  1.34 (0.19), residues: 737
  sheet: -0.95 (1.06), residues: 29
  loop : -1.83 (0.38), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 165 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.019   0.002   PHE A 308 
 TYR   0.012   0.001   TYR A  87 
 ARG   0.003   0.000   ARG B 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2212.92 seconds
wall clock time: 39 minutes 13.77 seconds (2353.77 seconds total)