Starting phenix.real_space_refine
on Thu Mar  6 05:37:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zqi_11364/03_2025/6zqi_11364.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zqi_11364/03_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_11364/03_2025/6zqi_11364.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zqi_11364/03_2025/6zqi_11364.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zqi_11364/03_2025/6zqi_11364.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zqi_11364/03_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-5624/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: 4.19, per 1000 atoms: 0.83
  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: 1.47
  Conformation dependent library (CDL) restraints added in 669.7 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: 0.62
  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: 1.78

  Time building geometry restraints manager: 1.78 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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.540
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.200
-------------------------------------------------------------------------------
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  : 0.499 
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: 0.2249
  time to fit residues: 53.3520
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  : 0.527 
-------------------------------------------------------------------------------
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 = 40)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131067 restraints weight = 7365.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.135480 restraints weight = 4282.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.138533 restraints weight = 2989.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
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  : 0.603 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8384 (tp40) cc_final: 0.8062 (mt0)
REVERT: A   81 TYR cc_start: 0.8643 (t80) cc_final: 0.8234 (t80)
REVERT: A  178 GLU cc_start: 0.8179 (tp30) cc_final: 0.7609 (mm-30)
REVERT: A  201 ASP cc_start: 0.8232 (t0) cc_final: 0.7958 (t0)
REVERT: A  203 TYR cc_start: 0.8408 (m-10) cc_final: 0.8049 (m-80)
REVERT: A  221 ASP cc_start: 0.8195 (t70) cc_final: 0.7904 (t0)
REVERT: A  241 GLU cc_start: 0.8029 (mp0) cc_final: 0.7804 (mp0)
REVERT: A  365 VAL cc_start: 0.9225 (p) cc_final: 0.8982 (p)
REVERT: A  422 MET cc_start: 0.8670 (tpp) cc_final: 0.8079 (tpp)
REVERT: A  432 PHE cc_start: 0.7759 (m-10) cc_final: 0.4906 (p90)
REVERT: A  447 HIS cc_start: 0.8604 (t-90) cc_final: 0.8201 (t-170)
REVERT: A  455 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7311 (mptt)
REVERT: A  466 GLN cc_start: 0.8904 (mp10) cc_final: 0.8087 (pm20)
REVERT: A  471 PHE cc_start: 0.8602 (m-10) cc_final: 0.8045 (t80)
REVERT: B   32 ASN cc_start: 0.6987 (t0) cc_final: 0.6639 (t0)
REVERT: B   59 GLN cc_start: 0.8370 (mp10) cc_final: 0.8147 (mp10)
REVERT: C  127 GLU cc_start: 0.8558 (tt0) cc_final: 0.8263 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 170
  average time/residue: 0.2740
  time to fit residues: 60.6491
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  : 1.219 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 48 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.159940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.129132 restraints weight = 7480.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.133253 restraints weight = 4565.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.135890 restraints weight = 3282.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2605

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= 0.253
  Angle     :  0.672  18.932   6962  Z= 0.343
  Chirality :  0.046   0.314    773
  Planarity :  0.004   0.038    887
  Dihedral  :  5.737  79.721    724
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.79 %
    Favored  : 74.12 %
  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: -0.97 (0.32), residues: 649
  helix:  1.54 (0.47), residues: 132
  sheet: -0.29 (0.36), residues: 197
  loop : -1.88 (0.31), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP C 129 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.015   0.001   PHE A 454 
 TYR   0.015   0.002   TYR A  61 
 ARG   0.004   0.000   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
  176 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8743 (t80) cc_final: 0.8444 (t80)
REVERT: A  178 GLU cc_start: 0.8127 (tp30) cc_final: 0.7537 (mm-30)
REVERT: A  192 GLU cc_start: 0.8193 (mp0) cc_final: 0.7598 (mp0)
REVERT: A  201 ASP cc_start: 0.8219 (t0) cc_final: 0.7989 (t0)
REVERT: A  203 TYR cc_start: 0.8430 (m-10) cc_final: 0.8208 (m-80)
REVERT: A  221 ASP cc_start: 0.8185 (t70) cc_final: 0.7906 (t0)
REVERT: A  241 GLU cc_start: 0.8120 (mp0) cc_final: 0.7846 (mp0)
REVERT: A  301 LEU cc_start: 0.7965 (mt) cc_final: 0.7469 (mp)
REVERT: A  332 GLN cc_start: 0.6961 (tt0) cc_final: 0.6529 (tm-30)
REVERT: A  368 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7566 (mp0)
REVERT: A  412 PHE cc_start: 0.7734 (t80) cc_final: 0.7513 (t80)
REVERT: A  422 MET cc_start: 0.8674 (tpp) cc_final: 0.8105 (tpp)
REVERT: A  438 MET cc_start: 0.6396 (mpp) cc_final: 0.6013 (mpp)
REVERT: A  447 HIS cc_start: 0.8696 (t-90) cc_final: 0.8293 (t-170)
REVERT: A  471 PHE cc_start: 0.8637 (m-10) cc_final: 0.8040 (t80)
REVERT: B   32 ASN cc_start: 0.7054 (t0) cc_final: 0.6657 (t0)
  outliers start: 22
  outliers final: 18
  residues processed: 163
  average time/residue: 0.2639
  time to fit residues: 57.7304
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  151 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  296 LEU
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:   10.0000
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
A 227 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.154736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.123054 restraints weight = 7859.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.127148 restraints weight = 4667.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.130065 restraints weight = 3310.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.097   5144  Z= 0.424
  Angle     :  0.745  14.502   6962  Z= 0.391
  Chirality :  0.049   0.275    773
  Planarity :  0.005   0.042    887
  Dihedral  :  6.139  77.160    724
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 21.60 %
    Favored  : 72.25 %
  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: -1.19 (0.32), residues: 649
  helix:  0.93 (0.44), residues: 136
  sheet: -0.34 (0.37), residues: 199
  loop : -1.91 (0.31), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 226 
 HIS   0.006   0.001   HIS A 211 
 PHE   0.018   0.002   PHE A 219 
 TYR   0.025   0.002   TYR A  61 
 ARG   0.003   0.001   ARG A 247 

*********************** 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
  179 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8604 (mm110) cc_final: 0.8330 (mm-40)
REVERT: A   81 TYR cc_start: 0.8420 (t80) cc_final: 0.7921 (t80)
REVERT: A  178 GLU cc_start: 0.7939 (tp30) cc_final: 0.7644 (mm-30)
REVERT: A  192 GLU cc_start: 0.8371 (mp0) cc_final: 0.7540 (mp0)
REVERT: A  201 ASP cc_start: 0.8371 (t0) cc_final: 0.8104 (t0)
REVERT: A  221 ASP cc_start: 0.8315 (t70) cc_final: 0.8013 (t0)
REVERT: A  412 PHE cc_start: 0.7702 (t80) cc_final: 0.7467 (t80)
REVERT: A  422 MET cc_start: 0.8723 (tpp) cc_final: 0.7963 (tpp)
REVERT: A  438 MET cc_start: 0.6559 (mpp) cc_final: 0.6061 (mpp)
REVERT: A  471 PHE cc_start: 0.8794 (m-10) cc_final: 0.8140 (t80)
REVERT: B   32 ASN cc_start: 0.7183 (t0) cc_final: 0.6980 (t0)
REVERT: B   44 MET cc_start: 0.7629 (tpp) cc_final: 0.7413 (tpp)
REVERT: C  128 ASN cc_start: 0.8098 (t0) cc_final: 0.7775 (t0)
  outliers start: 33
  outliers final: 24
  residues processed: 163
  average time/residue: 0.1788
  time to fit residues: 37.4020
Evaluate side-chains
  161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 ILE
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  179 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  296 LEU
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
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   41 ILE
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 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:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 43 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0070
   chunk 4 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.1402

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.157082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.126138 restraints weight = 7611.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.130339 restraints weight = 4467.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.133264 restraints weight = 3157.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   5144  Z= 0.250
  Angle     :  0.688  20.996   6962  Z= 0.353
  Chirality :  0.047   0.315    773
  Planarity :  0.004   0.041    887
  Dihedral  :  5.813  79.095    724
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 24.77 %
    Favored  : 69.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.32), residues: 649
  helix:  1.54 (0.47), residues: 131
  sheet: -0.32 (0.38), residues: 190
  loop : -1.86 (0.30), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 226 
 HIS   0.006   0.001   HIS A 227 
 PHE   0.018   0.001   PHE A 454 
 TYR   0.015   0.002   TYR A  61 
 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
  181 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 151
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 TYR cc_start: 0.8350 (t80) cc_final: 0.7988 (t80)
REVERT: A  178 GLU cc_start: 0.8003 (tp30) cc_final: 0.7631 (mm-30)
REVERT: A  192 GLU cc_start: 0.8335 (mp0) cc_final: 0.7511 (mp0)
REVERT: A  201 ASP cc_start: 0.8353 (t0) cc_final: 0.8066 (t0)
REVERT: A  221 ASP cc_start: 0.8303 (t70) cc_final: 0.8042 (t0)
REVERT: A  293 ARG cc_start: 0.8420 (ttp-110) cc_final: 0.8046 (ttp-110)
REVERT: A  412 PHE cc_start: 0.7713 (t80) cc_final: 0.7491 (t80)
REVERT: A  422 MET cc_start: 0.8705 (tpp) cc_final: 0.8053 (tpp)
REVERT: A  438 MET cc_start: 0.6356 (mpp) cc_final: 0.5849 (mpp)
REVERT: A  471 PHE cc_start: 0.8658 (m-10) cc_final: 0.7986 (t80)
REVERT: B   32 ASN cc_start: 0.7062 (t0) cc_final: 0.6829 (t0)
REVERT: B   44 MET cc_start: 0.7593 (tpp) cc_final: 0.7351 (tpp)
REVERT: C  161 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7524 (mm)
  outliers start: 30
  outliers final: 21
  residues processed: 168
  average time/residue: 0.1692
  time to fit residues: 36.8844
Evaluate side-chains
  161 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 139
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
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  179 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  350 THR
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain B residue   12 MET
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 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:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.154015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.122946 restraints weight = 7585.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.127189 restraints weight = 4490.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.130084 restraints weight = 3174.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   5144  Z= 0.309
  Angle     :  0.699  15.041   6962  Z= 0.366
  Chirality :  0.047   0.264    773
  Planarity :  0.004   0.042    887
  Dihedral  :  5.877  79.294    724
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 25.33 %
    Favored  : 69.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.32), residues: 649
  helix:  1.31 (0.46), residues: 136
  sheet: -0.29 (0.37), residues: 198
  loop : -1.93 (0.31), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.022   0.002   PHE A 454 
 TYR   0.019   0.002   TYR A  61 
 ARG   0.003   0.000   ARG C 151 

*********************** 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
  172 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 142
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8424 (mm-40)
REVERT: A   81 TYR cc_start: 0.8475 (t80) cc_final: 0.8175 (t80)
REVERT: A  178 GLU cc_start: 0.7886 (tp30) cc_final: 0.7455 (mm-30)
REVERT: A  192 GLU cc_start: 0.8388 (mp0) cc_final: 0.7571 (mp0)
REVERT: A  201 ASP cc_start: 0.8345 (t0) cc_final: 0.8071 (t0)
REVERT: A  221 ASP cc_start: 0.8238 (t70) cc_final: 0.8007 (t0)
REVERT: A  350 THR cc_start: 0.9289 (OUTLIER) cc_final: 0.8933 (t)
REVERT: A  412 PHE cc_start: 0.7814 (t80) cc_final: 0.7600 (t80)
REVERT: A  422 MET cc_start: 0.8677 (tpp) cc_final: 0.8237 (tpp)
REVERT: A  438 MET cc_start: 0.6377 (mpp) cc_final: 0.5946 (mpp)
REVERT: A  471 PHE cc_start: 0.8821 (m-10) cc_final: 0.8090 (t80)
REVERT: B   32 ASN cc_start: 0.6699 (t0) cc_final: 0.6394 (t0)
REVERT: C  161 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7810 (mm)
  outliers start: 30
  outliers final: 23
  residues processed: 160
  average time/residue: 0.2238
  time to fit residues: 46.1576
Evaluate side-chains
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   48 THR
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  258 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  350 THR
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
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 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:    2.9990
   chunk 59 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.6984

-------------------------------------------------------------------------------
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 = 0.3881 r_free = 0.3881 target = 0.157291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.126422 restraints weight = 7369.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.130760 restraints weight = 4308.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.133747 restraints weight = 3016.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3677

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= 0.195
  Angle     :  0.713  23.117   6962  Z= 0.361
  Chirality :  0.047   0.320    773
  Planarity :  0.004   0.040    887
  Dihedral  :  5.695  80.719    724
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 26.82 %
    Favored  : 68.72 %
  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: -0.76 (0.32), residues: 649
  helix:  1.89 (0.48), residues: 131
  sheet: -0.01 (0.39), residues: 185
  loop : -1.87 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 212 
 HIS   0.006   0.001   HIS A  27 
 PHE   0.019   0.001   PHE A 454 
 TYR   0.010   0.001   TYR A  61 
 ARG   0.003   0.000   ARG C 151 

*********************** 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
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 136
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8391 (mm-40)
REVERT: A  178 GLU cc_start: 0.7960 (tp30) cc_final: 0.7494 (mm-30)
REVERT: A  192 GLU cc_start: 0.8306 (mp0) cc_final: 0.7423 (mp0)
REVERT: A  412 PHE cc_start: 0.7822 (t80) cc_final: 0.7606 (t80)
REVERT: A  422 MET cc_start: 0.8603 (tpp) cc_final: 0.8180 (tpp)
REVERT: A  438 MET cc_start: 0.6065 (mpp) cc_final: 0.5716 (mpp)
REVERT: A  471 PHE cc_start: 0.8793 (m-10) cc_final: 0.8028 (t80)
REVERT: B   32 ASN cc_start: 0.6657 (t0) cc_final: 0.6448 (t0)
REVERT: B   84 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7591 (tptp)
REVERT: C  161 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7822 (mm)
  outliers start: 24
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1828
  time to fit residues: 35.6539
Evaluate side-chains
  150 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue   40 THR
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  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0570
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5896

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.159110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.128080 restraints weight = 7583.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.132447 restraints weight = 4403.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.135443 restraints weight = 3076.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5144  Z= 0.179
  Angle     :  0.668  18.277   6962  Z= 0.348
  Chirality :  0.046   0.294    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.557  80.738    724
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 26.82 %
    Favored  : 68.16 %
  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: -0.57 (0.33), residues: 649
  helix:  2.04 (0.48), residues: 131
  sheet:  0.13 (0.39), residues: 187
  loop : -1.77 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.017   0.001   PHE A 454 
 TYR   0.010   0.001   TYR B  60 
 ARG   0.004   0.000   ARG B  33 

*********************** 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
  165 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8624 (mm-40) cc_final: 0.8376 (mm-40)
REVERT: A  178 GLU cc_start: 0.8061 (tp30) cc_final: 0.7667 (mm-30)
REVERT: A  192 GLU cc_start: 0.8370 (mp0) cc_final: 0.7602 (mp0)
REVERT: A  412 PHE cc_start: 0.7830 (t80) cc_final: 0.7618 (t80)
REVERT: A  422 MET cc_start: 0.8519 (tpp) cc_final: 0.8058 (tpp)
REVERT: A  438 MET cc_start: 0.6055 (mpp) cc_final: 0.5726 (mpp)
REVERT: A  471 PHE cc_start: 0.8797 (m-10) cc_final: 0.8028 (t80)
REVERT: B   32 ASN cc_start: 0.6582 (t0) cc_final: 0.6360 (t0)
REVERT: B   84 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7580 (tptp)
REVERT: C  161 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8188 (mm)
  outliers start: 27
  outliers final: 21
  residues processed: 152
  average time/residue: 0.1825
  time to fit residues: 36.7357
Evaluate side-chains
  149 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 1.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
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  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0770
   chunk 49 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 60 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   overall best weight:    1.1742

-------------------------------------------------------------------------------
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**
A 447 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.155639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124714 restraints weight = 7456.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.128850 restraints weight = 4387.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.131798 restraints weight = 3112.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   5144  Z= 0.253
  Angle     :  0.728  19.529   6962  Z= 0.376
  Chirality :  0.048   0.324    773
  Planarity :  0.004   0.040    887
  Dihedral  :  5.685  79.828    724
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 28.49 %
    Favored  : 67.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.33), residues: 649
  helix:  2.06 (0.48), residues: 131
  sheet:  0.07 (0.39), residues: 185
  loop : -1.82 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.021   0.002   PHE A 454 
 TYR   0.014   0.002   TYR A  61 
 ARG   0.004   0.001   ARG B  33 

*********************** 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
  156 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 GLU cc_start: 0.7859 (tp30) cc_final: 0.7372 (mm-30)
REVERT: A  192 GLU cc_start: 0.8431 (mp0) cc_final: 0.7651 (mp0)
REVERT: A  412 PHE cc_start: 0.7823 (t80) cc_final: 0.7607 (t80)
REVERT: A  422 MET cc_start: 0.8516 (tpp) cc_final: 0.8073 (tpp)
REVERT: A  438 MET cc_start: 0.6485 (mpp) cc_final: 0.6054 (mpp)
REVERT: A  471 PHE cc_start: 0.8782 (m-10) cc_final: 0.8076 (t80)
REVERT: B   84 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7627 (tptp)
REVERT: C  161 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7779 (mm)
  outliers start: 23
  outliers final: 19
  residues processed: 146
  average time/residue: 0.1606
  time to fit residues: 30.3410
Evaluate side-chains
  147 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
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  258 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
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 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:    6.9990
   chunk 7 optimal weight:    0.0670
   chunk 3 optimal weight:    0.1980
   chunk 21 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0980
   chunk 39 optimal weight:    0.4980
   chunk 0 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.2918

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.160107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.128896 restraints weight = 7398.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.133256 restraints weight = 4318.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.136259 restraints weight = 3035.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5144  Z= 0.162
  Angle     :  0.696  17.798   6962  Z= 0.353
  Chirality :  0.046   0.275    773
  Planarity :  0.004   0.039    887
  Dihedral  :  5.465  80.800    724
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 29.80 %
    Favored  : 67.23 %
  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: -0.51 (0.33), residues: 649
  helix:  2.19 (0.47), residues: 131
  sheet:  0.15 (0.39), residues: 185
  loop : -1.76 (0.31), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 212 
 HIS   0.004   0.001   HIS A  27 
 PHE   0.017   0.001   PHE A 454 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.008   0.000   ARG B  33 

********************** 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
  160 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8304 (mm-40)
REVERT: A  178 GLU cc_start: 0.7955 (tp30) cc_final: 0.7330 (mm-30)
REVERT: A  192 GLU cc_start: 0.8332 (mp0) cc_final: 0.7591 (mp0)
REVERT: A  412 PHE cc_start: 0.7795 (t80) cc_final: 0.7579 (t80)
REVERT: A  422 MET cc_start: 0.8485 (tpp) cc_final: 0.7905 (tpp)
REVERT: A  455 LYS cc_start: 0.7762 (ttmt) cc_final: 0.6927 (mmtm)
REVERT: A  468 LEU cc_start: 0.8814 (mt) cc_final: 0.8548 (mm)
REVERT: A  471 PHE cc_start: 0.8783 (m-10) cc_final: 0.8018 (t80)
REVERT: B   32 ASN cc_start: 0.6463 (t0) cc_final: 0.6087 (t0)
REVERT: B   33 ARG cc_start: 0.7388 (ptm-80) cc_final: 0.7140 (ptm-80)
REVERT: B   84 LYS cc_start: 0.8374 (mtmt) cc_final: 0.7668 (tptp)
REVERT: C  161 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7686 (mm)
  outliers start: 16
  outliers final: 14
  residues processed: 153
  average time/residue: 0.2438
  time to fit residues: 47.7133
Evaluate side-chains
  149 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 134
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 THR
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  250 HIS
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  367 THR
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue   22 VAL
Chi-restraints excluded: chain B residue   52 GLU
Chi-restraints excluded: chain B residue   77 VAL
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:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 28 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 164 ASN
** 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 = 0.3899 r_free = 0.3899 target = 0.158700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.127478 restraints weight = 7545.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.131740 restraints weight = 4398.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134521 restraints weight = 3091.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5144  Z= 0.197
  Angle     :  0.713  18.406   6962  Z= 0.362
  Chirality :  0.047   0.306    773
  Planarity :  0.004   0.041    887
  Dihedral  :  5.452  80.016    724
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 29.42 %
    Favored  : 67.04 %
  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 (0.33), residues: 649
  helix:  2.12 (0.47), residues: 132
  sheet:  0.10 (0.38), residues: 187
  loop : -1.75 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 212 
 HIS   0.005   0.001   HIS A  27 
 PHE   0.018   0.001   PHE A 498 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.008   0.001   ARG B  33 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2530.31 seconds
wall clock time: 48 minutes 16.86 seconds (2896.86 seconds total)