Starting phenix.real_space_refine
on Tue Feb 11 09:33:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zqi_11364/02_2025/6zqi_11364.cif"
  }
  resolution = 3.8
  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=   0.005
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      43      5.16       5
     C    3167      2.51       5
     N     875      2.21       5
     O     947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5032
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 3835
          Classifications: {'peptide': 504}
          Link IDs: {'PTRANS': 12, 'TRANS': 491}
    Chain: "B"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 790
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 6, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 393
          Classifications: {'peptide': 50}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.44, per 1000 atoms: 0.68
  Number of scatterers: 5032
  At special positions: 0
  Unit cell: (74.36, 123.37, 138.58, 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      43     16.00
     O     947      8.00
     N     875      7.00
     C    3167      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   3 " - pdb=" SG  CYS A  30 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 105 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS A 116 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 292 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 309 " - pdb=" SG  CYS A 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  34 " - pdb=" SG  CYS B  69 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  45 " - pdb=" SG  CYS B  81 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  53 " - pdb=" SG  CYS B  67 " distance=2.04

  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
  Links applied
    NAG-ASN
      " NAG B 201 " - " ASN B  70 "
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 601.4 milliseconds
  

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1182

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      23.4% alpha, 29.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 82 through 86
      removed outlier: 3.808A  pdb=" N   ALA A  86 " --> pdb=" O   ASP A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 104
    Processing helix  chain 'A' and resid 131 through 133
      No H-bonds generated for 'chain 'A' and resid 131 through 133'
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.603A  pdb=" N   HIS A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 216 through 220'
    Processing helix  chain 'A' and resid 240 through 242
      No H-bonds generated for 'chain 'A' and resid 240 through 242'
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 392 through 396
      removed outlier: 3.598A  pdb=" N   THR A 395 " --> pdb=" O   THR A 392 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LYS A 396 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 392 through 396'
    Processing helix  chain 'A' and resid 406 through 425
    Processing helix  chain 'A' and resid 437 through 458
      removed outlier: 5.797A  pdb=" N   SER A 452 " --> pdb=" O   GLN A 448 " (cutoff:3.500A)
      removed outlier: 5.750A  pdb=" N   ALA A 453 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ALA A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 479
      removed outlier: 3.538A  pdb=" N   LEU A 468 " --> pdb=" O   PHE A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 502
      removed outlier: 3.726A  pdb=" N   PHE A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 133
    Processing helix  chain 'C' and resid 133 through 146
      removed outlier: 4.026A  pdb=" N   THR C 146 " --> pdb=" O   VAL C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 150 through 165
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 13
      removed outlier: 7.173A  pdb=" N   ARG A 138 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   THR A  48 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   GLU A 136 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
      removed outlier: 3.690A  pdb=" N   GLU A 277 " --> pdb=" O   THR A 284 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 25
      removed outlier: 3.926A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 228
      removed outlier: 7.034A  pdb=" N   GLY A 127 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   SER A  58 " --> pdb=" O   LEU A 125 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   LEU A 125 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   CYS A  60 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   LYS A 123 " --> pdb=" O   CYS A  60 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   GLU A  62 " --> pdb=" O   CYS A 121 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   CYS A 121 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 274 " --> pdb=" O   LEU A 213 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 73
    Processing sheet with id=AA6, first strand: chain 'A' and resid 244 through 246
    Processing sheet with id=AA7, first strand: chain 'A' and resid 307 through 308
      removed outlier: 6.641A  pdb=" N   ALA A 307 " --> pdb=" O   LYS A 341 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 315
      removed outlier: 3.568A  pdb=" N   SER A 320 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 315
      removed outlier: 3.965A  pdb=" N   ARG A 358 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 347
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2 through 5
      removed outlier: 6.199A  pdb=" N   TYR B  10 " --> pdb=" O   TRP B  75 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL B  77 " --> pdb=" O   TYR B  10 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   MET B  12 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   GLY B  79 " --> pdb=" O   MET B  12 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 23 through 26

    213 hydrogen bonds defined for protein.
    576 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: 1.55

  Time building geometry restraints manager: 1.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1646
        1.35 -     1.47: 1271
        1.47 -     1.59: 2159
        1.59 -     1.71: 0
        1.71 -     1.83: 68
  Bond restraints: 5144
  Sorted by residual:
  bond pdb=" N   ARG B  94 "
       pdb=" CA  ARG B  94 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.23e-02 6.61e+03 5.30e+00
  bond pdb=" N   HIS A 250 "
       pdb=" CA  HIS A 250 "
    ideal  model  delta    sigma   weight residual
    1.455  1.482 -0.028 1.25e-02 6.40e+03 4.94e+00
  bond pdb=" N   HIS B 101 "
       pdb=" CA  HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.68e+00
  bond pdb=" CE1 HIS A 250 "
       pdb=" NE2 HIS A 250 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.22e+00
  bond pdb=" CE1 HIS B 101 "
       pdb=" NE2 HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.19e+00
  ... (remaining 5139 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 6902
        2.47 -     4.93: 54
        4.93 -     7.40: 4
        7.40 -     9.86: 0
        9.86 -    12.33: 2
  Bond angle restraints: 6962
  Sorted by residual:
  angle pdb=" CA  CYS A 116 "
        pdb=" CB  CYS A 116 "
        pdb=" SG  CYS A 116 "
      ideal   model   delta    sigma   weight residual
     114.40  126.73  -12.33 2.30e+00 1.89e-01 2.87e+01
  angle pdb=" CA  CYS A  92 "
        pdb=" CB  CYS A  92 "
        pdb=" SG  CYS A  92 "
      ideal   model   delta    sigma   weight residual
     114.40  125.70  -11.30 2.30e+00 1.89e-01 2.41e+01
  angle pdb=" N   CYS A 116 "
        pdb=" CA  CYS A 116 "
        pdb=" C   CYS A 116 "
      ideal   model   delta    sigma   weight residual
     109.52  114.59   -5.07 1.55e+00 4.16e-01 1.07e+01
  angle pdb=" C   SER B  71 "
        pdb=" N   THR B  72 "
        pdb=" CA  THR B  72 "
      ideal   model   delta    sigma   weight residual
     122.32  127.75   -5.43 1.76e+00 3.23e-01 9.52e+00
  angle pdb=" C   LYS A 444 "
        pdb=" N   PHE A 445 "
        pdb=" CA  PHE A 445 "
      ideal   model   delta    sigma   weight residual
     120.68  116.13    4.55 1.70e+00 3.46e-01 7.16e+00
  ... (remaining 6957 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2817
       17.87 -    35.75: 189
       35.75 -    53.62: 39
       53.62 -    71.50: 6
       71.50 -    89.37: 5
  Dihedral angle restraints: 3056
    sinusoidal: 1203
      harmonic: 1853
  Sorted by residual:
  dihedral pdb=" CB  CYS A  74 "
           pdb=" SG  CYS A  74 "
           pdb=" SG  CYS A 105 "
           pdb=" CB  CYS A 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.58  -87.42     1      1.00e+01 1.00e-02 9.17e+01
  dihedral pdb=" CB  CYS B  53 "
           pdb=" SG  CYS B  53 "
           pdb=" SG  CYS B  67 "
           pdb=" CB  CYS B  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -23.78  -62.22     1      1.00e+01 1.00e-02 5.13e+01
  dihedral pdb=" CB  CYS B  34 "
           pdb=" SG  CYS B  34 "
           pdb=" SG  CYS B  69 "
           pdb=" CB  CYS B  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.93  -57.07     1      1.00e+01 1.00e-02 4.38e+01
  ... (remaining 3053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 602
       0.048 -    0.097: 137
       0.097 -    0.145: 30
       0.145 -    0.193: 3
       0.193 -    0.241: 1
  Chirality restraints: 773
  Sorted by residual:
  chirality pdb=" CA  CYS A 116 "
            pdb=" N   CYS A 116 "
            pdb=" C   CYS A 116 "
            pdb=" CB  CYS A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.46e+00
  chirality pdb=" CA  CYS A  92 "
            pdb=" N   CYS A  92 "
            pdb=" C   CYS A  92 "
            pdb=" CB  CYS A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.74e-01
  chirality pdb=" CA  ARG B  94 "
            pdb=" N   ARG B  94 "
            pdb=" C   ARG B  94 "
            pdb=" CB  ARG B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 770 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  74 "   -0.021 5.00e-02 4.00e+02   3.23e-02 1.66e+00
        pdb=" N   PRO A  75 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A  75 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  75 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  45 "    0.018 5.00e-02 4.00e+02   2.69e-02 1.16e+00
        pdb=" N   PRO B  46 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B  46 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  46 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B  53 "   -0.017 5.00e-02 4.00e+02   2.62e-02 1.10e+00
        pdb=" N   PRO B  54 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO B  54 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B  54 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1744
        2.85 -     3.36: 4336
        3.36 -     3.87: 7621
        3.87 -     4.39: 8126
        4.39 -     4.90: 14511
  Nonbonded interactions: 36338
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 380 "
            pdb=" NH1 ARG A 403 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" OG1 THR A 322 "
            pdb=" OG1 THR A 326 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   ILE A 497 "
            pdb=" OG1 THR A 501 "
     model   vdw
     2.370 3.040
  nonbonded pdb=" OE1 GLU A 178 "
            pdb=" OG  SER A 188 "
     model   vdw
     2.385 3.040
  nonbonded pdb=" O   SER A 369 "
            pdb=" OG  SER A 369 "
     model   vdw
     2.389 3.040
  ... (remaining 36333 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.930
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
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      :  0.002   0.031   5144  Z= 0.163
  Angle     :  0.565  12.331   6962  Z= 0.325
  Chirality :  0.044   0.241    773
  Planarity :  0.003   0.032    887
  Dihedral  : 12.439  89.370   1847
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  3.72 %
    Favored  : 95.16 %
  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: -2.14 (0.29), residues: 649
  helix: -0.02 (0.42), residues: 132
  sheet: -0.56 (0.35), residues: 197
  loop : -2.67 (0.27), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 226 
 HIS   0.002   0.000   HIS A 160 
 PHE   0.017   0.001   PHE A 445 
 TYR   0.010   0.001   TYR A  61 
 ARG   0.003   0.000   ARG B  93 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 189
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.7547 (mtm) cc_final: 0.7152 (mtm)
REVERT: A   77 GLN cc_start: 0.8105 (tp40) cc_final: 0.7776 (mt0)
REVERT: A   81 TYR cc_start: 0.8482 (t80) cc_final: 0.8174 (t80)
REVERT: A  178 GLU cc_start: 0.7788 (tp30) cc_final: 0.7464 (mm-30)
REVERT: A  201 ASP cc_start: 0.8099 (t0) cc_final: 0.7829 (t0)
REVERT: A  209 ASN cc_start: 0.8389 (t0) cc_final: 0.8050 (t0)
REVERT: A  221 ASP cc_start: 0.7948 (t70) cc_final: 0.7688 (t0)
REVERT: A  330 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: A  374 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8178 (mmtm)
REVERT: A  422 MET cc_start: 0.8617 (tpp) cc_final: 0.8021 (tpp)
REVERT: A  432 PHE cc_start: 0.7640 (m-10) cc_final: 0.4941 (p90)
REVERT: A  447 HIS cc_start: 0.8448 (t-90) cc_final: 0.7942 (t-170)
REVERT: A  455 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7000 (mptt)
REVERT: A  471 PHE cc_start: 0.8609 (m-10) cc_final: 0.7968 (t80)
REVERT: B   32 ASN cc_start: 0.6953 (t0) cc_final: 0.6699 (t0)
REVERT: B   39 MET cc_start: 0.7032 (ptt) cc_final: 0.6826 (ttt)
REVERT: B  101 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7546 (m-70)
REVERT: C  127 GLU cc_start: 0.8549 (tt0) cc_final: 0.8067 (mt-10)
  outliers start: 6
  outliers final: 1
  residues processed: 192
  average time/residue: 0.2445
  time to fit residues: 58.6249
Evaluate side-chains
  150 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 148
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain B residue  101 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.4980
   chunk 37 optimal weight:    0.3980
   chunk 59 optimal weight:    0.4980
   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 131 GLN
A 363 ASN
** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 153 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.161951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131065 restraints weight = 7365.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.135429 restraints weight = 4282.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.138528 restraints weight = 3002.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   5144  Z= 0.268
  Angle     :  0.672  15.630   6962  Z= 0.347
  Chirality :  0.047   0.295    773
  Planarity :  0.004   0.035    887
  Dihedral  :  5.925  77.604    726
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 16.01 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.28 (0.31), residues: 649
  helix:  1.23 (0.46), residues: 131
  sheet: -0.35 (0.36), residues: 196
  loop : -2.14 (0.29), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.013   0.001   PHE A 219 
 TYR   0.015   0.001   TYR A  61 
 ARG   0.006   0.001   ARG C 151 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 159
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8367 (tp40) cc_final: 0.8054 (mt0)
REVERT: A   81 TYR cc_start: 0.8636 (t80) cc_final: 0.8233 (t80)
REVERT: A  178 GLU cc_start: 0.8168 (tp30) cc_final: 0.7600 (mm-30)
REVERT: A  201 ASP cc_start: 0.8230 (t0) cc_final: 0.7956 (t0)
REVERT: A  203 TYR cc_start: 0.8403 (m-10) cc_final: 0.8049 (m-80)
REVERT: A  221 ASP cc_start: 0.8186 (t70) cc_final: 0.7898 (t0)
REVERT: A  241 GLU cc_start: 0.8018 (mp0) cc_final: 0.7795 (mp0)
REVERT: A  365 VAL cc_start: 0.9223 (p) cc_final: 0.8980 (p)
REVERT: A  422 MET cc_start: 0.8670 (tpp) cc_final: 0.8080 (tpp)
REVERT: A  432 PHE cc_start: 0.7752 (m-10) cc_final: 0.4908 (p90)
REVERT: A  447 HIS cc_start: 0.8606 (t-90) cc_final: 0.8200 (t-170)
REVERT: A  455 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7317 (mptt)
REVERT: A  466 GLN cc_start: 0.8901 (mp10) cc_final: 0.8082 (pm20)
REVERT: A  471 PHE cc_start: 0.8592 (m-10) cc_final: 0.8042 (t80)
REVERT: B   32 ASN cc_start: 0.6980 (t0) cc_final: 0.6629 (t0)
REVERT: B   59 GLN cc_start: 0.8362 (mp10) cc_final: 0.8140 (mp10)
REVERT: C  127 GLU cc_start: 0.8555 (tt0) cc_final: 0.8258 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 170
  average time/residue: 0.1823
  time to fit residues: 39.8129
Evaluate side-chains
  159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 144
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  130 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0970
   chunk 48 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 144 HIS
B  59 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.158788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.127980 restraints weight = 7507.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132084 restraints weight = 4599.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.134944 restraints weight = 3295.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5144  Z= 0.281
  Angle     :  0.689  19.520   6962  Z= 0.352
  Chirality :  0.047   0.315    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.837  79.587    724
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 21.79 %
    Favored  : 73.37 %
  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: -0.98 (0.32), residues: 649
  helix:  1.54 (0.46), residues: 131
  sheet: -0.29 (0.36), residues: 195
  loop : -1.86 (0.31), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP C 129 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.016   0.002   PHE B  25 
 TYR   0.016   0.002   TYR A  61 
 ARG   0.004   0.001   ARG C 151 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8779 (t80) cc_final: 0.8455 (t80)
REVERT: A  178 GLU cc_start: 0.8102 (tp30) cc_final: 0.7564 (mm-30)
REVERT: A  192 GLU cc_start: 0.8244 (mp0) cc_final: 0.7567 (mp0)
REVERT: A  201 ASP cc_start: 0.8243 (t0) cc_final: 0.7996 (t0)
REVERT: A  221 ASP cc_start: 0.8197 (t70) cc_final: 0.7920 (t0)
REVERT: A  241 GLU cc_start: 0.8171 (mp0) cc_final: 0.7877 (mp0)
REVERT: A  301 LEU cc_start: 0.7996 (mt) cc_final: 0.7502 (mp)
REVERT: A  332 GLN cc_start: 0.6989 (tt0) cc_final: 0.6452 (tm-30)
REVERT: A  368 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7595 (mp0)
REVERT: A  412 PHE cc_start: 0.7736 (t80) cc_final: 0.7519 (t80)
REVERT: A  422 MET cc_start: 0.8671 (tpp) cc_final: 0.8118 (tpp)
REVERT: A  438 MET cc_start: 0.6498 (mpp) cc_final: 0.6106 (mpp)
REVERT: A  447 HIS cc_start: 0.8580 (t-90) cc_final: 0.8112 (t-170)
REVERT: A  471 PHE cc_start: 0.8634 (m-10) cc_final: 0.8039 (t80)
REVERT: B   32 ASN cc_start: 0.7093 (t0) cc_final: 0.6702 (t0)
  outliers start: 26
  outliers final: 19
  residues processed: 165
  average time/residue: 0.1700
  time to fit residues: 36.1066
Evaluate side-chains
  159 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 139
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue   92 CYS
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0970
   chunk 54 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 42 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0970
   overall best weight:    0.4976

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.163012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.131269 restraints weight = 7607.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.135754 restraints weight = 4416.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.138840 restraints weight = 3087.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   5144  Z= 0.159
  Angle     :  0.587  13.130   6962  Z= 0.307
  Chirality :  0.044   0.218    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.569  80.007    724
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.91 %
    Favored  : 73.00 %
  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: -0.64 (0.32), residues: 649
  helix:  1.97 (0.48), residues: 131
  sheet:  0.00 (0.38), residues: 192
  loop : -1.76 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 129 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.016   0.001   PHE A 454 
 TYR   0.017   0.001   TYR A 203 
 ARG   0.003   0.000   ARG C 151 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8705 (t80) cc_final: 0.8356 (t80)
REVERT: A  178 GLU cc_start: 0.8150 (tp30) cc_final: 0.7595 (mm-30)
REVERT: A  192 GLU cc_start: 0.8099 (mp0) cc_final: 0.7205 (mp0)
REVERT: A  201 ASP cc_start: 0.8420 (t0) cc_final: 0.8017 (t0)
REVERT: A  221 ASP cc_start: 0.8200 (t70) cc_final: 0.7927 (t0)
REVERT: A  241 GLU cc_start: 0.8146 (mp0) cc_final: 0.7816 (mp0)
REVERT: A  412 PHE cc_start: 0.7661 (t80) cc_final: 0.7424 (t80)
REVERT: A  422 MET cc_start: 0.8566 (tpp) cc_final: 0.7968 (tpp)
REVERT: A  438 MET cc_start: 0.6318 (mpp) cc_final: 0.5998 (mpp)
REVERT: A  447 HIS cc_start: 0.8706 (t-90) cc_final: 0.8281 (t-170)
REVERT: A  466 GLN cc_start: 0.9008 (mp10) cc_final: 0.8752 (pm20)
REVERT: A  471 PHE cc_start: 0.8641 (m-10) cc_final: 0.8030 (t80)
REVERT: B   32 ASN cc_start: 0.6823 (t0) cc_final: 0.6506 (t0)
REVERT: C  161 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8270 (mm)
  outliers start: 22
  outliers final: 16
  residues processed: 161
  average time/residue: 0.1946
  time to fit residues: 40.2500
Evaluate side-chains
  165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  151 MET
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.159663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.128157 restraints weight = 7470.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.132492 restraints weight = 4375.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135488 restraints weight = 3090.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5144  Z= 0.211
  Angle     :  0.651  20.448   6962  Z= 0.334
  Chirality :  0.046   0.303    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.499  80.380    724
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 23.46 %
    Favored  : 71.32 %
  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: -0.71 (0.32), residues: 649
  helix:  2.01 (0.47), residues: 131
  sheet: -0.01 (0.37), residues: 192
  loop : -1.89 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.012   0.001   PHE A 454 
 TYR   0.017   0.001   TYR A 306 
 ARG   0.003   0.000   ARG C 151 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8508 (t80) cc_final: 0.8077 (t80)
REVERT: A  178 GLU cc_start: 0.8045 (tp30) cc_final: 0.7586 (mm-30)
REVERT: A  192 GLU cc_start: 0.8125 (mp0) cc_final: 0.7227 (mp0)
REVERT: A  201 ASP cc_start: 0.8398 (t0) cc_final: 0.8048 (t0)
REVERT: A  203 TYR cc_start: 0.8438 (m-10) cc_final: 0.8203 (m-80)
REVERT: A  204 TYR cc_start: 0.8526 (t80) cc_final: 0.8323 (t80)
REVERT: A  221 ASP cc_start: 0.8191 (t70) cc_final: 0.7920 (t0)
REVERT: A  368 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7436 (mp0)
REVERT: A  412 PHE cc_start: 0.7682 (t80) cc_final: 0.7448 (t80)
REVERT: A  422 MET cc_start: 0.8522 (tpp) cc_final: 0.8012 (tpp)
REVERT: A  438 MET cc_start: 0.6429 (mpp) cc_final: 0.5997 (mpp)
REVERT: A  447 HIS cc_start: 0.8756 (t-90) cc_final: 0.8284 (t-170)
REVERT: A  454 PHE cc_start: 0.7757 (t80) cc_final: 0.7553 (t80)
REVERT: A  455 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7240 (mptt)
REVERT: A  466 GLN cc_start: 0.8921 (mp10) cc_final: 0.8665 (pm20)
REVERT: A  471 PHE cc_start: 0.8630 (m-10) cc_final: 0.8010 (t80)
REVERT: C  161 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7706 (mm)
  outliers start: 28
  outliers final: 19
  residues processed: 170
  average time/residue: 0.1653
  time to fit residues: 36.3800
Evaluate side-chains
  162 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 141
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0010
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 153 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.160979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.129796 restraints weight = 7502.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.134064 restraints weight = 4410.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.137070 restraints weight = 3098.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5144  Z= 0.174
  Angle     :  0.620  14.818   6962  Z= 0.321
  Chirality :  0.045   0.267    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.473  81.200    724
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 25.33 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 (0.32), residues: 649
  helix:  2.13 (0.47), residues: 131
  sheet:  0.14 (0.38), residues: 192
  loop : -1.79 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.012   0.001   PHE B  25 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.003   0.000   ARG B  33 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8528 (t80) cc_final: 0.8101 (t80)
REVERT: A  178 GLU cc_start: 0.8103 (tp30) cc_final: 0.7471 (mm-30)
REVERT: A  192 GLU cc_start: 0.8190 (mp0) cc_final: 0.7271 (mp0)
REVERT: A  201 ASP cc_start: 0.8395 (t0) cc_final: 0.8039 (t0)
REVERT: A  203 TYR cc_start: 0.8439 (m-10) cc_final: 0.8198 (m-80)
REVERT: A  221 ASP cc_start: 0.8185 (t70) cc_final: 0.7890 (t0)
REVERT: A  368 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7415 (mp0)
REVERT: A  412 PHE cc_start: 0.7673 (t80) cc_final: 0.7443 (t80)
REVERT: A  422 MET cc_start: 0.8511 (tpp) cc_final: 0.8010 (tpp)
REVERT: A  447 HIS cc_start: 0.8776 (t-90) cc_final: 0.8294 (t-170)
REVERT: A  466 GLN cc_start: 0.8914 (mp10) cc_final: 0.8651 (pm20)
REVERT: A  471 PHE cc_start: 0.8650 (m-10) cc_final: 0.8039 (t80)
REVERT: B   32 ASN cc_start: 0.6598 (t0) cc_final: 0.6066 (t0)
REVERT: B   56 LEU cc_start: 0.9009 (pt) cc_final: 0.8807 (pp)
REVERT: C  161 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8045 (mm)
  outliers start: 25
  outliers final: 17
  residues processed: 156
  average time/residue: 0.1505
  time to fit residues: 30.6691
Evaluate side-chains
  155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 36 optimal weight:    0.0020
   chunk 59 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0030
   chunk 17 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 55 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.162161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.131186 restraints weight = 7343.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.135503 restraints weight = 4312.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.138465 restraints weight = 3037.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5144  Z= 0.160
  Angle     :  0.653  23.012   6962  Z= 0.332
  Chirality :  0.046   0.309    773
  Planarity :  0.003   0.036    887
  Dihedral  :  5.389  82.001    724
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 25.70 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.41 (0.32), residues: 649
  helix:  2.28 (0.47), residues: 131
  sheet:  0.20 (0.38), residues: 192
  loop : -1.73 (0.30), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.016   0.001   PHE A 454 
 TYR   0.016   0.001   TYR A 204 
 ARG   0.002   0.000   ARG B  33 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8546 (t80) cc_final: 0.8065 (t80)
REVERT: A  178 GLU cc_start: 0.8140 (tp30) cc_final: 0.7434 (tp30)
REVERT: A  192 GLU cc_start: 0.8186 (mp0) cc_final: 0.7293 (mp0)
REVERT: A  201 ASP cc_start: 0.8577 (t0) cc_final: 0.8344 (t0)
REVERT: A  221 ASP cc_start: 0.8198 (t70) cc_final: 0.7898 (t0)
REVERT: A  368 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7428 (mp0)
REVERT: A  412 PHE cc_start: 0.7754 (t80) cc_final: 0.7521 (t80)
REVERT: A  422 MET cc_start: 0.8504 (tpp) cc_final: 0.7968 (tpp)
REVERT: A  447 HIS cc_start: 0.8785 (t-90) cc_final: 0.8291 (t-170)
REVERT: A  455 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7243 (mptt)
REVERT: A  461 MET cc_start: 0.4722 (mpp) cc_final: 0.4242 (mpp)
REVERT: A  466 GLN cc_start: 0.8924 (mp10) cc_final: 0.8607 (pm20)
REVERT: A  471 PHE cc_start: 0.8689 (m-10) cc_final: 0.8056 (t80)
REVERT: B   32 ASN cc_start: 0.6484 (t0) cc_final: 0.5977 (t0)
REVERT: C  161 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8139 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1576
  time to fit residues: 33.1552
Evaluate side-chains
  166 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0270
   chunk 37 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.1242

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

Flipped N/Q/H residues before XYZ refinement:
A 227 HIS
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.157763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126764 restraints weight = 7516.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.130927 restraints weight = 4460.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.133909 restraints weight = 3170.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   5144  Z= 0.239
  Angle     :  0.686  18.620   6962  Z= 0.353
  Chirality :  0.046   0.307    773
  Planarity :  0.004   0.036    887
  Dihedral  :  5.602  80.557    724
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 25.70 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.41 (0.33), residues: 649
  helix:  2.17 (0.46), residues: 131
  sheet:  0.19 (0.38), residues: 192
  loop : -1.67 (0.31), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.016   0.001   PHE A 454 
 TYR   0.023   0.002   TYR A 203 
 ARG   0.002   0.000   ARG A   2 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8487 (t80) cc_final: 0.7998 (t80)
REVERT: A  178 GLU cc_start: 0.8072 (tp30) cc_final: 0.7598 (mm-30)
REVERT: A  192 GLU cc_start: 0.8269 (mp0) cc_final: 0.7434 (mp0)
REVERT: A  201 ASP cc_start: 0.8533 (t0) cc_final: 0.8095 (t0)
REVERT: A  203 TYR cc_start: 0.8515 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  221 ASP cc_start: 0.8218 (t70) cc_final: 0.7926 (t0)
REVERT: A  368 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7443 (mp0)
REVERT: A  412 PHE cc_start: 0.7709 (t80) cc_final: 0.7479 (t80)
REVERT: A  422 MET cc_start: 0.8526 (tpp) cc_final: 0.7963 (tpp)
REVERT: A  455 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7181 (mptt)
REVERT: A  461 MET cc_start: 0.4822 (mpp) cc_final: 0.4354 (mpp)
REVERT: A  471 PHE cc_start: 0.8669 (m-10) cc_final: 0.8019 (t80)
REVERT: B   32 ASN cc_start: 0.6639 (t0) cc_final: 0.6184 (t0)
REVERT: C  161 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8182 (mm)
  outliers start: 22
  outliers final: 19
  residues processed: 154
  average time/residue: 0.1665
  time to fit residues: 33.7718
Evaluate side-chains
  155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  376 MET
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 59 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3882 r_free = 0.3882 target = 0.157416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126636 restraints weight = 7421.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.130814 restraints weight = 4401.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.133723 restraints weight = 3119.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5144  Z= 0.237
  Angle     :  0.741  20.166   6962  Z= 0.375
  Chirality :  0.047   0.327    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.722  80.263    724
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 25.70 %
    Favored  : 70.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.47 (0.33), residues: 649
  helix:  2.13 (0.46), residues: 132
  sheet:  0.10 (0.38), residues: 198
  loop : -1.70 (0.31), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.016   0.001   PHE A 454 
 TYR   0.028   0.002   TYR A 306 
 ARG   0.002   0.000   ARG A   2 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 GLU cc_start: 0.7921 (tp30) cc_final: 0.7295 (mm-30)
REVERT: A  192 GLU cc_start: 0.8278 (mp0) cc_final: 0.7389 (mp0)
REVERT: A  201 ASP cc_start: 0.8557 (t0) cc_final: 0.8118 (t0)
REVERT: A  203 TYR cc_start: 0.8551 (m-80) cc_final: 0.8309 (m-80)
REVERT: A  221 ASP cc_start: 0.8220 (t70) cc_final: 0.7927 (t0)
REVERT: A  368 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7417 (mp0)
REVERT: A  412 PHE cc_start: 0.7720 (t80) cc_final: 0.7495 (t80)
REVERT: A  422 MET cc_start: 0.8523 (tpp) cc_final: 0.7960 (tpp)
REVERT: A  455 LYS cc_start: 0.7819 (ttmt) cc_final: 0.7188 (mptt)
REVERT: A  461 MET cc_start: 0.4845 (mpp) cc_final: 0.4374 (mpp)
REVERT: A  471 PHE cc_start: 0.8741 (m-10) cc_final: 0.8019 (t80)
REVERT: B   32 ASN cc_start: 0.6717 (t0) cc_final: 0.6313 (t0)
REVERT: C  161 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7816 (mm)
  outliers start: 23
  outliers final: 21
  residues processed: 149
  average time/residue: 0.1470
  time to fit residues: 29.0020
Evaluate side-chains
  155 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   66 ASP
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3900 r_free = 0.3900 target = 0.159844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.128988 restraints weight = 7406.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.133136 restraints weight = 4332.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.136133 restraints weight = 3058.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5144  Z= 0.195
  Angle     :  0.695  17.830   6962  Z= 0.356
  Chirality :  0.046   0.289    773
  Planarity :  0.004   0.037    887
  Dihedral  :  5.668  80.479    724
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 25.88 %
    Favored  : 69.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.39 (0.33), residues: 649
  helix:  2.26 (0.46), residues: 132
  sheet:  0.25 (0.39), residues: 188
  loop : -1.71 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.016   0.001   PHE A 454 
 TYR   0.026   0.002   TYR A 306 
 ARG   0.002   0.000   ARG C 151 

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

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

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1298 Ramachandran restraints generated.
    649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 142
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8582 (mm-40) cc_final: 0.7965 (mm-40)
REVERT: A  178 GLU cc_start: 0.7950 (tp30) cc_final: 0.7700 (tp30)
REVERT: A  190 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7176 (tt0)
REVERT: A  192 GLU cc_start: 0.8373 (mp0) cc_final: 0.7549 (mp0)
REVERT: A  201 ASP cc_start: 0.8605 (t0) cc_final: 0.8163 (t0)
REVERT: A  221 ASP cc_start: 0.8211 (t70) cc_final: 0.7923 (t0)
REVERT: A  368 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7375 (mp0)
REVERT: A  412 PHE cc_start: 0.7776 (t80) cc_final: 0.7557 (t80)
REVERT: A  422 MET cc_start: 0.8508 (tpp) cc_final: 0.7958 (tpp)
REVERT: A  455 LYS cc_start: 0.7785 (ttmt) cc_final: 0.7195 (mptt)
REVERT: A  461 MET cc_start: 0.4782 (mpp) cc_final: 0.4313 (mpp)
REVERT: A  471 PHE cc_start: 0.8753 (m-10) cc_final: 0.8022 (t80)
REVERT: B   32 ASN cc_start: 0.6662 (t0) cc_final: 0.6276 (t0)
REVERT: B   60 TYR cc_start: 0.8942 (m-80) cc_final: 0.8464 (m-80)
REVERT: C  161 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8120 (mm)
  outliers start: 23
  outliers final: 18
  residues processed: 154
  average time/residue: 0.1447
  time to fit residues: 29.3973
Evaluate side-chains
  158 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  139 VAL
Chi-restraints excluded: chain A residue  189 MET
Chi-restraints excluded: chain A residue  202 LEU
Chi-restraints excluded: chain A residue  214 VAL
Chi-restraints excluded: chain A residue  250 HIS
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   69 CYS
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain C residue  131 LEU
Chi-restraints excluded: chain C residue  139 VAL
Chi-restraints excluded: chain C residue  161 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0870
   chunk 63 optimal weight:    0.5980
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** A 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 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 = 0.3911 r_free = 0.3911 target = 0.159973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.128829 restraints weight = 7477.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.133082 restraints weight = 4337.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.136125 restraints weight = 3047.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5144  Z= 0.178
  Angle     :  0.697  18.514   6962  Z= 0.353
  Chirality :  0.046   0.285    773
  Planarity :  0.003   0.036    887
  Dihedral  :  5.574  80.417    724
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 26.26 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -0.19 (0.33), residues: 649
  helix:  2.59 (0.47), residues: 126
  sheet:  0.37 (0.38), residues: 198
  loop : -1.63 (0.32), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP C 129 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.017   0.001   PHE A 454 
 TYR   0.025   0.002   TYR A 203 
 ARG   0.002   0.000   ARG C 151 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2014.59 seconds
wall clock time: 37 minutes 4.87 seconds (2224.87 seconds total)