Starting phenix.real_space_refine
on Thu Jun  5 04:55:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r1d_14239/06_2025/7r1d_14239.cif"
  }
  resolution = 3.5
  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=   0.003
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      19      5.16       5
     C    3279      2.51       5
     N     904      2.21       5
     O     981      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 5183
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1549
          Classifications: {'peptide': 192}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 3206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 405, 3206
          Classifications: {'peptide': 405}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 22, 'TRANS': 382}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 19
    Chain: "B"
      Number of atoms: 428
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 428
          Classifications: {'peptide': 56}
          Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 7, 'TRANS': 48}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 3.52, per 1000 atoms: 0.68
  Number of scatterers: 5183
  At special positions: 0
  Unit cell: (68.04, 85.05, 99.792, 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      19     16.00
     O     981      8.00
     N     904      7.00
     C    3279      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.29
  Conformation dependent library (CDL) restraints added in 636.1 milliseconds
  

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1234

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 12 sheets defined
      21.4% alpha, 24.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'C' and resid 96 through 114
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.608A  pdb=" N   TRP C 126 " --> pdb=" O   CYS C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 140 through 150
    Processing helix  chain 'C' and resid 159 through 169
      removed outlier: 3.717A  pdb=" N   LYS C 165 " --> pdb=" O   VAL C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 199
    Processing helix  chain 'C' and resid 281 through 286
      removed outlier: 3.548A  pdb=" N   PHE C 285 " --> pdb=" O   PRO C 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 27
    Processing helix  chain 'A' and resid 27 through 31
      removed outlier: 4.253A  pdb=" N   LEU A  31 " --> pdb=" O   ASN A  27 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 27 through 31'
    Processing helix  chain 'A' and resid 348 through 350
      No H-bonds generated for 'chain 'A' and resid 348 through 350'
    Processing helix  chain 'A' and resid 356 through 360
      removed outlier: 3.892A  pdb=" N   ALA A 359 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 409
    Processing helix  chain 'B' and resid 107 through 109
      No H-bonds generated for 'chain 'B' and resid 107 through 109'
    Processing helix  chain 'B' and resid 114 through 125
      removed outlier: 4.116A  pdb=" N   ILE B 118 " --> pdb=" O   PRO B 114 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 157 through 158
      removed outlier: 3.856A  pdb=" N   PHE A  93 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 216 through 217
      removed outlier: 3.769A  pdb=" N   MET C 280 " --> pdb=" O   ILE C 216 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 267
      removed outlier: 6.958A  pdb=" N   THR C 251 " --> pdb=" O   VAL C 245 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   VAL C 245 " --> pdb=" O   THR C 251 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ARG C 253 " --> pdb=" O   ASP C 243 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 39
      removed outlier: 3.982A  pdb=" N   ILE A 398 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP A 379 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49
      removed outlier: 3.660A  pdb=" N   GLN A  48 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASN A  77 " --> pdb=" O   HIS A 123 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   HIS A 123 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ILE A 119 " --> pdb=" O   ILE A  81 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   SER A  83 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 5.744A  pdb=" N   ILE A 117 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 63
    Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 133
      removed outlier: 5.561A  pdb=" N   ILE A 139 " --> pdb=" O   MET A 133 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ARG A 172 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 183 through 185
    Processing sheet with id=AA9, first strand: chain 'A' and resid 230 through 235
      removed outlier: 3.737A  pdb=" N   ALA A 247 " --> pdb=" O   LYS A 251 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LYS A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 281
      removed outlier: 3.608A  pdb=" N   CYS A 278 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   HIS A 311 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 325
      removed outlier: 6.664A  pdb=" N   ASP A 346 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
      removed outlier: 5.764A  pdb=" N   LEU A 366 " --> pdb=" O   ASP A 346 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99
      removed outlier: 3.792A  pdb=" N   ILE B  97 " --> pdb=" O   VAL B 104 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   VAL B 104 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    495 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: 1.37

  Time building geometry restraints manager: 1.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1664
        1.34 -     1.45: 788
        1.45 -     1.57: 2838
        1.57 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 5317
  Sorted by residual:
  bond pdb=" CA  GLU A 286 "
       pdb=" C   GLU A 286 "
    ideal  model  delta    sigma   weight residual
    1.523  1.497  0.027 1.80e-02 3.09e+03 2.20e+00
  bond pdb=" CB  PRO C 173 "
       pdb=" CG  PRO C 173 "
    ideal  model  delta    sigma   weight residual
    1.492  1.565 -0.073 5.00e-02 4.00e+02 2.13e+00
  bond pdb=" CD1 TYR A  98 "
       pdb=" CE1 TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.382  1.342  0.040 3.00e-02 1.11e+03 1.79e+00
  bond pdb=" CB  TYR A  98 "
       pdb=" CG  TYR A  98 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.20e-02 2.07e+03 1.49e+00
  bond pdb=" CA  ILE A  81 "
       pdb=" C   ILE A  81 "
    ideal  model  delta    sigma   weight residual
    1.527  1.518  0.009 8.50e-03 1.38e+04 1.11e+00
  ... (remaining 5312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.40: 7080
        2.40 -     4.81: 121
        4.81 -     7.21: 17
        7.21 -     9.61: 2
        9.61 -    12.02: 2
  Bond angle restraints: 7222
  Sorted by residual:
  angle pdb=" C   HIS A  97 "
        pdb=" N   TYR A  98 "
        pdb=" CA  TYR A  98 "
      ideal   model   delta    sigma   weight residual
     121.54  111.77    9.77 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" C   LEU C 198 "
        pdb=" N   GLN C 199 "
        pdb=" CA  GLN C 199 "
      ideal   model   delta    sigma   weight residual
     122.56  114.04    8.52 1.72e+00 3.38e-01 2.45e+01
  angle pdb=" C   GLY A 107 "
        pdb=" N   PHE A 108 "
        pdb=" CA  PHE A 108 "
      ideal   model   delta    sigma   weight residual
     122.41  131.60   -9.19 2.09e+00 2.29e-01 1.93e+01
  angle pdb=" CA  PRO C 173 "
        pdb=" N   PRO C 173 "
        pdb=" CD  PRO C 173 "
      ideal   model   delta    sigma   weight residual
     112.00  106.57    5.43 1.40e+00 5.10e-01 1.51e+01
  angle pdb=" CA  LEU C 212 "
        pdb=" CB  LEU C 212 "
        pdb=" CG  LEU C 212 "
      ideal   model   delta    sigma   weight residual
     116.30  128.32  -12.02 3.50e+00 8.16e-02 1.18e+01
  ... (remaining 7217 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2844
       16.09 -    32.18: 270
       32.18 -    48.26: 50
       48.26 -    64.35: 18
       64.35 -    80.44: 3
  Dihedral angle restraints: 3185
    sinusoidal: 1288
      harmonic: 1897
  Sorted by residual:
  dihedral pdb=" CA  GLY A 107 "
           pdb=" C   GLY A 107 "
           pdb=" N   PHE A 108 "
           pdb=" CA  PHE A 108 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.22   27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  SER A 315 "
           pdb=" C   SER A 315 "
           pdb=" N   HIS A 316 "
           pdb=" CA  HIS A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.42   22.58     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CA  HIS A  78 "
           pdb=" C   HIS A  78 "
           pdb=" N   LEU A  79 "
           pdb=" CA  LEU A  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 3182 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 449
       0.033 -    0.067: 194
       0.067 -    0.100: 93
       0.100 -    0.133: 44
       0.133 -    0.167: 3
  Chirality restraints: 783
  Sorted by residual:
  chirality pdb=" CA  GLN C 199 "
            pdb=" N   GLN C 199 "
            pdb=" C   GLN C 199 "
            pdb=" CB  GLN C 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CA  THR A  28 "
            pdb=" N   THR A  28 "
            pdb=" C   THR A  28 "
            pdb=" CB  THR A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.06e-01
  chirality pdb=" CG  LEU C 212 "
            pdb=" CB  LEU C 212 "
            pdb=" CD1 LEU C 212 "
            pdb=" CD2 LEU C 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.44   -0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 780 not shown)

  Planarity restraints: 940
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 172 "    0.084 5.00e-02 4.00e+02   1.24e-01 2.47e+01
        pdb=" N   PRO C 173 "   -0.215 5.00e-02 4.00e+02
        pdb=" CA  PRO C 173 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO C 173 "    0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 107 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.15e+00
        pdb=" C   GLY A 107 "    0.039 2.00e-02 2.50e+03
        pdb=" O   GLY A 107 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   PHE A 108 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  24 "   -0.017 2.00e-02 2.50e+03   1.31e-02 4.31e+00
        pdb=" CG  TRP A  24 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  24 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  24 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  24 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  24 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  24 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  24 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  24 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  24 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 937 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 107
        2.66 -     3.22: 5036
        3.22 -     3.78: 8356
        3.78 -     4.34: 11320
        4.34 -     4.90: 18569
  Nonbonded interactions: 43388
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 227 "
            pdb=" OD1 ASN C 274 "
     model   vdw
     2.097 3.040
  nonbonded pdb=" NE2 GLN A  76 "
            pdb=" OD1 ASN A 122 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OD1 ASP A 379 "
            pdb=" N   PHE A 380 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" O   GLU A 275 "
            pdb=" OG  SER A 293 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" OH  TYR A 284 "
            pdb=" O   PRO A 327 "
     model   vdw
     2.190 3.040
  ... (remaining 43383 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:             0.610
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.890
  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:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   5317  Z= 0.217
  Angle     :  0.795  12.018   7222  Z= 0.432
  Chirality :  0.048   0.167    783
  Planarity :  0.006   0.124    940
  Dihedral  : 13.608  80.437   1951
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 17.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.32), residues: 645
  helix:  0.41 (0.49), residues: 121
  sheet: -1.10 (0.34), residues: 193
  loop : -1.14 (0.34), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A  24 
 HIS   0.005   0.001   HIS A  64 
 PHE   0.010   0.001   PHE A 243 
 TYR   0.021   0.002   TYR A 409 
 ARG   0.011   0.001   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21431 (  180)
  hydrogen bonds       : angle       8.72972 (  495)
  covalent geometry    : bond        0.00486 ( 5317)
  covalent geometry    : angle       0.79536 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.518 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9293 (tp) cc_final: 0.9038 (tp)
REVERT: C  111 ASN cc_start: 0.8693 (m-40) cc_final: 0.8381 (m-40)
REVERT: C  183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8353 (tt0)
REVERT: C  252 TYR cc_start: 0.8183 (m-80) cc_final: 0.7965 (m-80)
REVERT: A   33 ASP cc_start: 0.7141 (m-30) cc_final: 0.6819 (m-30)
REVERT: A   40 LEU cc_start: 0.9024 (mt) cc_final: 0.8779 (mt)
REVERT: A   72 THR cc_start: 0.8702 (m) cc_final: 0.8492 (m)
REVERT: A   79 LEU cc_start: 0.8577 (tp) cc_final: 0.8311 (tp)
REVERT: A  102 LYS cc_start: 0.7214 (mttt) cc_final: 0.6846 (mttt)
REVERT: A  282 ASN cc_start: 0.8648 (t0) cc_final: 0.7842 (t0)
REVERT: A  319 GLU cc_start: 0.7109 (tt0) cc_final: 0.6851 (mt-10)
REVERT: A  395 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7381 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1956
  time to fit residues: 34.6427
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.139405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108258 restraints weight = 9195.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.111946 restraints weight = 4786.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.114347 restraints weight = 3229.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5317  Z= 0.157
  Angle     :  0.702  10.137   7222  Z= 0.355
  Chirality :  0.048   0.163    783
  Planarity :  0.005   0.080    940
  Dihedral  :  5.544  23.213    695
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.49 %
    Favored  : 88.22 %
  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: -1.18 (0.32), residues: 645
  helix:  1.07 (0.48), residues: 116
  sheet: -1.39 (0.36), residues: 185
  loop : -1.02 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 121 
 HIS   0.006   0.001   HIS A 316 
 PHE   0.015   0.001   PHE C 256 
 TYR   0.017   0.002   TYR C 124 
 ARG   0.005   0.001   ARG A 341 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03511 (  180)
  hydrogen bonds       : angle       5.96043 (  495)
  covalent geometry    : bond        0.00357 ( 5317)
  covalent geometry    : angle       0.70231 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.580 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9325 (tp) cc_final: 0.9042 (tp)
REVERT: C  111 ASN cc_start: 0.8715 (m-40) cc_final: 0.8379 (m-40)
REVERT: C  163 TRP cc_start: 0.7729 (m100) cc_final: 0.7328 (m100)
REVERT: C  183 GLU cc_start: 0.8712 (tt0) cc_final: 0.8461 (tt0)
REVERT: C  192 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7470 (mtp85)
REVERT: A   24 TRP cc_start: 0.9071 (t60) cc_final: 0.8845 (t60)
REVERT: A   33 ASP cc_start: 0.7269 (m-30) cc_final: 0.6861 (m-30)
REVERT: A   79 LEU cc_start: 0.8522 (tp) cc_final: 0.8216 (tp)
REVERT: A  101 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7527 (pp20)
REVERT: A  102 LYS cc_start: 0.7325 (mttt) cc_final: 0.6783 (mttt)
REVERT: A  282 ASN cc_start: 0.8646 (t0) cc_final: 0.7864 (t0)
REVERT: A  311 HIS cc_start: 0.7855 (t70) cc_final: 0.7433 (t-90)
REVERT: A  319 GLU cc_start: 0.7412 (tt0) cc_final: 0.7003 (tt0)
REVERT: A  395 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7485 (mm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 126
  average time/residue: 0.1832
  time to fit residues: 31.3497
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  188 LEU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C 103 GLN
** B 125 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.138277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107048 restraints weight = 9294.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110703 restraints weight = 4818.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.113104 restraints weight = 3248.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5317  Z= 0.176
  Angle     :  0.685  10.321   7222  Z= 0.345
  Chirality :  0.048   0.156    783
  Planarity :  0.005   0.067    940
  Dihedral  :  5.393  25.341    695
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 13.71 %
    Favored  : 84.18 %
  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: -1.11 (0.32), residues: 645
  helix:  1.05 (0.48), residues: 122
  sheet: -1.33 (0.36), residues: 185
  loop : -1.00 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 122 
 HIS   0.005   0.001   HIS A 316 
 PHE   0.015   0.001   PHE C 256 
 TYR   0.015   0.002   TYR A 409 
 ARG   0.004   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03337 (  180)
  hydrogen bonds       : angle       5.68418 (  495)
  covalent geometry    : bond        0.00400 ( 5317)
  covalent geometry    : angle       0.68534 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9304 (tp) cc_final: 0.9014 (tp)
REVERT: C  111 ASN cc_start: 0.8731 (m-40) cc_final: 0.8393 (m-40)
REVERT: C  125 GLU cc_start: 0.8576 (tp30) cc_final: 0.8206 (tp30)
REVERT: C  127 PHE cc_start: 0.8419 (t80) cc_final: 0.7963 (t80)
REVERT: C  163 TRP cc_start: 0.7767 (m100) cc_final: 0.7204 (m100)
REVERT: A   24 TRP cc_start: 0.9048 (t60) cc_final: 0.8743 (t60)
REVERT: A   33 ASP cc_start: 0.7323 (m-30) cc_final: 0.6903 (m-30)
REVERT: A   79 LEU cc_start: 0.8596 (tp) cc_final: 0.8306 (tp)
REVERT: A  282 ASN cc_start: 0.8723 (t0) cc_final: 0.7881 (t0)
REVERT: A  395 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7468 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 121
  average time/residue: 0.1883
  time to fit residues: 30.7268
Evaluate side-chains
  114 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0040
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0070
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4210

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110441 restraints weight = 9409.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.114134 restraints weight = 4805.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.116622 restraints weight = 3195.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5317  Z= 0.123
  Angle     :  0.695  14.138   7222  Z= 0.336
  Chirality :  0.047   0.193    783
  Planarity :  0.004   0.057    940
  Dihedral  :  5.136  26.475    695
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 15.11 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.33), residues: 645
  helix:  1.21 (0.47), residues: 122
  sheet: -0.98 (0.35), residues: 200
  loop : -0.95 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP C 121 
 HIS   0.003   0.001   HIS A 316 
 PHE   0.015   0.001   PHE C 256 
 TYR   0.016   0.002   TYR A 409 
 ARG   0.003   0.000   ARG C 185 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  180)
  hydrogen bonds       : angle       5.31135 (  495)
  covalent geometry    : bond        0.00279 ( 5317)
  covalent geometry    : angle       0.69478 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.774 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9303 (tp) cc_final: 0.9020 (tp)
REVERT: C  111 ASN cc_start: 0.8701 (m-40) cc_final: 0.8350 (m-40)
REVERT: C  127 PHE cc_start: 0.8350 (t80) cc_final: 0.8009 (t80)
REVERT: C  163 TRP cc_start: 0.7843 (m100) cc_final: 0.7296 (m100)
REVERT: A   24 TRP cc_start: 0.9007 (t60) cc_final: 0.8707 (t60)
REVERT: A   33 ASP cc_start: 0.7373 (m-30) cc_final: 0.6917 (m-30)
REVERT: A   79 LEU cc_start: 0.8598 (tp) cc_final: 0.8366 (tp)
REVERT: A  282 ASN cc_start: 0.8594 (t0) cc_final: 0.7889 (t0)
REVERT: A  321 PHE cc_start: 0.8535 (m-80) cc_final: 0.8212 (m-80)
REVERT: A  395 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7346 (mm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 127
  average time/residue: 0.2100
  time to fit residues: 34.4744
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 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 = 0.3757 r_free = 0.3757 target = 0.134706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.105095 restraints weight = 9446.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.108733 restraints weight = 4732.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.111098 restraints weight = 3134.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   5317  Z= 0.262
  Angle     :  0.754  13.980   7222  Z= 0.375
  Chirality :  0.049   0.205    783
  Planarity :  0.005   0.058    940
  Dihedral  :  5.515  27.332    695
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.64 %
    Favored  : 81.20 %
  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: 645
  helix:  1.20 (0.48), residues: 122
  sheet: -1.17 (0.36), residues: 179
  loop : -1.10 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 122 
 HIS   0.004   0.001   HIS A 373 
 PHE   0.023   0.002   PHE C 256 
 TYR   0.018   0.002   TYR A  98 
 ARG   0.007   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03486 (  180)
  hydrogen bonds       : angle       5.64652 (  495)
  covalent geometry    : bond        0.00590 ( 5317)
  covalent geometry    : angle       0.75363 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.621 
Fit side-chains
REVERT: C  109 LEU cc_start: 0.9327 (tp) cc_final: 0.9060 (tp)
REVERT: C  111 ASN cc_start: 0.8830 (m-40) cc_final: 0.8492 (m-40)
REVERT: C  163 TRP cc_start: 0.8063 (m100) cc_final: 0.7696 (m100)
REVERT: A   33 ASP cc_start: 0.7469 (m-30) cc_final: 0.7114 (m-30)
REVERT: A   79 LEU cc_start: 0.8697 (tp) cc_final: 0.8447 (tp)
REVERT: A  282 ASN cc_start: 0.8876 (t0) cc_final: 0.7993 (t0)
REVERT: A  316 HIS cc_start: 0.8243 (OUTLIER) cc_final: 0.7935 (m-70)
REVERT: A  395 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7386 (mm-30)
  outliers start: 18
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1570
  time to fit residues: 25.4697
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  183 GLU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
C 130 ASN
** C 199 GLN ** 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 = 0.3747 r_free = 0.3747 target = 0.133981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.103833 restraints weight = 9389.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.107488 restraints weight = 4771.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.109934 restraints weight = 3185.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   5317  Z= 0.255
  Angle     :  0.778  13.917   7222  Z= 0.382
  Chirality :  0.049   0.182    783
  Planarity :  0.005   0.057    940
  Dihedral  :  5.623  28.178    695
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.22 %
    Favored  : 79.61 %
  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: -1.15 (0.32), residues: 645
  helix:  1.17 (0.48), residues: 116
  sheet: -1.21 (0.37), residues: 179
  loop : -1.16 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 122 
 HIS   0.004   0.001   HIS A 226 
 PHE   0.027   0.002   PHE C 256 
 TYR   0.024   0.002   TYR A  98 
 ARG   0.007   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03382 (  180)
  hydrogen bonds       : angle       5.63880 (  495)
  covalent geometry    : bond        0.00577 ( 5317)
  covalent geometry    : angle       0.77766 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9343 (tp) cc_final: 0.9080 (tp)
REVERT: C  111 ASN cc_start: 0.8817 (m-40) cc_final: 0.8491 (m-40)
REVERT: C  163 TRP cc_start: 0.8117 (m100) cc_final: 0.7782 (m100)
REVERT: A   33 ASP cc_start: 0.7395 (m-30) cc_final: 0.7009 (m-30)
REVERT: A   79 LEU cc_start: 0.8712 (tp) cc_final: 0.8469 (tp)
REVERT: A  282 ASN cc_start: 0.8878 (t0) cc_final: 0.7983 (t0)
REVERT: A  395 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7424 (mm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 123
  average time/residue: 0.1605
  time to fit residues: 26.1700
Evaluate side-chains
  118 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  183 GLU
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue   72 THR
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 15 optimal weight:    0.1980
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 199 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 = 0.3804 r_free = 0.3804 target = 0.138112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.108052 restraints weight = 9233.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111820 restraints weight = 4694.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.114232 restraints weight = 3131.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5317  Z= 0.145
  Angle     :  0.723  13.552   7222  Z= 0.352
  Chirality :  0.047   0.170    783
  Planarity :  0.004   0.051    940
  Dihedral  :  5.284  26.803    695
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 18.80 %
    Favored  : 78.56 %
  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: -0.89 (0.33), residues: 645
  helix:  1.11 (0.48), residues: 122
  sheet: -0.93 (0.35), residues: 193
  loop : -0.97 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 373 
 PHE   0.022   0.001   PHE C 256 
 TYR   0.020   0.002   TYR C 124 
 ARG   0.007   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02988 (  180)
  hydrogen bonds       : angle       5.31985 (  495)
  covalent geometry    : bond        0.00334 ( 5317)
  covalent geometry    : angle       0.72311 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9320 (tp) cc_final: 0.9027 (tp)
REVERT: C  111 ASN cc_start: 0.8754 (m-40) cc_final: 0.8400 (m-40)
REVERT: C  127 PHE cc_start: 0.8497 (t80) cc_final: 0.8238 (t80)
REVERT: C  163 TRP cc_start: 0.8029 (m100) cc_final: 0.7593 (m100)
REVERT: C  192 ARG cc_start: 0.8367 (mtm110) cc_final: 0.7914 (mtp85)
REVERT: C  196 ARG cc_start: 0.7227 (ptp-170) cc_final: 0.6819 (mtt90)
REVERT: C  200 GLN cc_start: 0.6593 (OUTLIER) cc_final: 0.6188 (mp10)
REVERT: A   33 ASP cc_start: 0.7394 (m-30) cc_final: 0.6966 (m-30)
REVERT: A   79 LEU cc_start: 0.8681 (tp) cc_final: 0.8461 (tp)
REVERT: A  282 ASN cc_start: 0.8704 (t0) cc_final: 0.7867 (t0)
REVERT: A  316 HIS cc_start: 0.8042 (OUTLIER) cc_final: 0.7551 (m170)
REVERT: A  321 PHE cc_start: 0.8678 (m-80) cc_final: 0.8227 (m-80)
REVERT: A  395 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7383 (mm-30)
  outliers start: 15
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1609
  time to fit residues: 26.5282
Evaluate side-chains
  123 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.3794 r_free = 0.3794 target = 0.137596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.107538 restraints weight = 9291.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.111330 restraints weight = 4728.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.113763 restraints weight = 3146.803|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5317  Z= 0.164
  Angle     :  0.750  13.331   7222  Z= 0.363
  Chirality :  0.048   0.186    783
  Planarity :  0.004   0.050    940
  Dihedral  :  5.299  29.794    695
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 19.16 %
    Favored  : 78.38 %
  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: -0.90 (0.33), residues: 645
  helix:  1.22 (0.48), residues: 122
  sheet: -0.97 (0.35), residues: 193
  loop : -1.00 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 316 
 PHE   0.022   0.001   PHE C 256 
 TYR   0.018   0.002   TYR C 124 
 ARG   0.006   0.000   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03148 (  180)
  hydrogen bonds       : angle       5.33345 (  495)
  covalent geometry    : bond        0.00378 ( 5317)
  covalent geometry    : angle       0.74971 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9316 (tp) cc_final: 0.9023 (tp)
REVERT: C  111 ASN cc_start: 0.8756 (m-40) cc_final: 0.8401 (m-40)
REVERT: C  127 PHE cc_start: 0.8507 (t80) cc_final: 0.8242 (t80)
REVERT: C  163 TRP cc_start: 0.8064 (m100) cc_final: 0.7704 (m100)
REVERT: C  200 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6128 (mp10)
REVERT: A   33 ASP cc_start: 0.7375 (m-30) cc_final: 0.6980 (m-30)
REVERT: A   79 LEU cc_start: 0.8642 (tp) cc_final: 0.8430 (tp)
REVERT: A  282 ASN cc_start: 0.8724 (t0) cc_final: 0.7879 (t0)
REVERT: A  321 PHE cc_start: 0.8694 (m-80) cc_final: 0.8228 (m-80)
REVERT: A  395 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7363 (mm-30)
  outliers start: 14
  outliers final: 13
  residues processed: 118
  average time/residue: 0.1668
  time to fit residues: 26.0158
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0670
   chunk 42 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6918

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.138116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.107718 restraints weight = 9189.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.111445 restraints weight = 4710.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113862 restraints weight = 3151.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5317  Z= 0.152
  Angle     :  0.742  14.422   7222  Z= 0.359
  Chirality :  0.048   0.182    783
  Planarity :  0.004   0.049    940
  Dihedral  :  5.226  30.018    695
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.68 %
    Favored  : 77.33 %
  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: -0.92 (0.32), residues: 645
  helix:  1.15 (0.48), residues: 122
  sheet: -0.97 (0.35), residues: 193
  loop : -1.00 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 316 
 PHE   0.012   0.001   PHE A 108 
 TYR   0.018   0.002   TYR C 124 
 ARG   0.006   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03089 (  180)
  hydrogen bonds       : angle       5.26454 (  495)
  covalent geometry    : bond        0.00352 ( 5317)
  covalent geometry    : angle       0.74170 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9299 (tp) cc_final: 0.9003 (tp)
REVERT: C  111 ASN cc_start: 0.8746 (m-40) cc_final: 0.8397 (m-40)
REVERT: C  127 PHE cc_start: 0.8504 (t80) cc_final: 0.8235 (t80)
REVERT: C  163 TRP cc_start: 0.8060 (m100) cc_final: 0.7756 (m100)
REVERT: C  192 ARG cc_start: 0.8413 (mtm110) cc_final: 0.8067 (mtp85)
REVERT: C  196 ARG cc_start: 0.7188 (ptp-170) cc_final: 0.6479 (ptp-170)
REVERT: C  200 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6171 (mp10)
REVERT: A   33 ASP cc_start: 0.7367 (m-30) cc_final: 0.6932 (m-30)
REVERT: A  108 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7412 (m-80)
REVERT: A  282 ASN cc_start: 0.8685 (t0) cc_final: 0.7838 (t0)
REVERT: A  321 PHE cc_start: 0.8640 (m-80) cc_final: 0.8175 (m-80)
REVERT: A  395 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7406 (mm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 123
  average time/residue: 0.1713
  time to fit residues: 27.5916
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   chunk 3 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.137805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.107449 restraints weight = 9208.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.111236 restraints weight = 4657.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113694 restraints weight = 3092.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   5317  Z= 0.156
  Angle     :  0.756  14.192   7222  Z= 0.366
  Chirality :  0.048   0.182    783
  Planarity :  0.004   0.049    940
  Dihedral  :  5.203  29.934    695
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.86 %
    Favored  : 77.15 %
  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: -0.93 (0.32), residues: 645
  helix:  1.03 (0.47), residues: 122
  sheet: -0.94 (0.35), residues: 192
  loop : -0.98 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 122 
 HIS   0.003   0.001   HIS A 226 
 PHE   0.012   0.001   PHE A 108 
 TYR   0.018   0.002   TYR C 124 
 ARG   0.007   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03166 (  180)
  hydrogen bonds       : angle       5.31614 (  495)
  covalent geometry    : bond        0.00371 ( 5317)
  covalent geometry    : angle       0.75610 ( 7222)

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
REVERT: C  109 LEU cc_start: 0.9292 (tp) cc_final: 0.9006 (tp)
REVERT: C  111 ASN cc_start: 0.8700 (m-40) cc_final: 0.8353 (m-40)
REVERT: C  127 PHE cc_start: 0.8497 (t80) cc_final: 0.8216 (t80)
REVERT: C  163 TRP cc_start: 0.8041 (m100) cc_final: 0.7716 (m100)
REVERT: C  192 ARG cc_start: 0.8385 (mtm110) cc_final: 0.7994 (mpp80)
REVERT: C  196 ARG cc_start: 0.7180 (ptp-170) cc_final: 0.6615 (mtt90)
REVERT: C  200 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6187 (mp10)
REVERT: A   33 ASP cc_start: 0.7398 (m-30) cc_final: 0.6987 (m-30)
REVERT: A  108 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7388 (m-80)
REVERT: A  282 ASN cc_start: 0.8663 (t0) cc_final: 0.7823 (t0)
REVERT: A  321 PHE cc_start: 0.8631 (m-80) cc_final: 0.8154 (m-80)
REVERT: A  395 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7421 (mm-30)
  outliers start: 17
  outliers final: 14
  residues processed: 123
  average time/residue: 0.1717
  time to fit residues: 27.5830
Evaluate side-chains
  125 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  200 GLN
Chi-restraints excluded: chain C residue  254 VAL
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain C residue  259 THR
Chi-restraints excluded: chain C residue  266 ILE
Chi-restraints excluded: chain A residue   28 THR
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  108 PHE
Chi-restraints excluded: chain A residue  114 LYS
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  227 THR
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  338 THR
Chi-restraints excluded: chain A residue  391 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 58 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0070
   chunk 15 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0870
   chunk 17 optimal weight:    0.2980
   chunk 54 optimal weight:    0.0470
   chunk 30 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.1274

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.145172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.114197 restraints weight = 9197.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.118049 restraints weight = 4779.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.120559 restraints weight = 3209.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   5317  Z= 0.118
  Angle     :  0.739  14.174   7222  Z= 0.357
  Chirality :  0.047   0.182    783
  Planarity :  0.004   0.046    940
  Dihedral  :  4.909  30.204    695
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.04 %
    Favored  : 77.15 %
  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: -0.87 (0.32), residues: 645
  helix:  1.06 (0.47), residues: 122
  sheet: -0.82 (0.35), residues: 192
  loop : -1.00 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 122 
 HIS   0.002   0.001   HIS A 328 
 PHE   0.012   0.001   PHE A 108 
 TYR   0.019   0.002   TYR C 124 
 ARG   0.006   0.001   ARG C 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03029 (  180)
  hydrogen bonds       : angle       5.05261 (  495)
  covalent geometry    : bond        0.00280 ( 5317)
  covalent geometry    : angle       0.73943 ( 7222)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2214.65 seconds
wall clock time: 40 minutes 15.66 seconds (2415.66 seconds total)