Starting phenix.real_space_refine
on Fri Aug 22 15:19:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kep_37163/08_2025/8kep_37163.map"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.012
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      21      5.16       5
     C    3060      2.51       5
     N     825      2.21       5
     O     928      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4834
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1615
          Classifications: {'peptide': 215}
          Link IDs: {'PTRANS': 12, 'TRANS': 202}
    Chain: "L"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1645
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 12, 'TRANS': 198}
    Chain: "A"
      Number of atoms: 1574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1574
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
  Time building chain proxies: 1.16, per 1000 atoms: 0.24
  Number of scatterers: 4834
  At special positions: 0
  Unit cell: (74.97, 72.59, 138.04, 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      21     16.00
     O     928      8.00
     N     825      7.00
     C    3060      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 101 " - pdb=" SG  CYS H 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 148 " - pdb=" SG  CYS H 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 135 " - pdb=" SG  CYS L 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 152.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1154

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 13 sheets defined
      4.3% alpha, 26.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'H' and resid 164 through 166
      No H-bonds generated for 'chain 'H' and resid 164 through 166'
    Processing helix  chain 'L' and resid 122 through 129
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 368 through 372
      removed outlier: 3.809A  pdb=" N   ALA A 372 " --> pdb=" O   TYR A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.565A  pdb=" N   GLN A 409 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 410 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 406 through 410'
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
      removed outlier: 3.534A  pdb=" N   VAL H  18 " --> pdb=" O   LEU H  83 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR H  80 " --> pdb=" O   THR H  71 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   THR H  71 " --> pdb=" O   TYR H  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.890A  pdb=" N   TRP H  50 " --> pdb=" O   ASP H  59 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ASP H  59 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 128 through 132
      removed outlier: 3.506A  pdb=" N   SER H 128 " --> pdb=" O   LYS H 151 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS H 151 " --> pdb=" O   SER H 128 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   LEU H 132 " --> pdb=" O   GLY H 147 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   GLY H 147 " --> pdb=" O   LEU H 132 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER H 188 " --> pdb=" O   CYS H 148 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL H 189 " --> pdb=" O   HIS H 172 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   HIS H 172 " --> pdb=" O   VAL H 189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 158 through 162
      removed outlier: 3.612A  pdb=" N   THR H 159 " --> pdb=" O   ASN H 207 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 177 through 178
      removed outlier: 3.737A  pdb=" N   VAL H 177 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.628A  pdb=" N   ARG L  24 " --> pdb=" O   THR L   5 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.678A  pdb=" N   GLU L 106 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR L 103 " --> pdb=" O   TYR L  87 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE L  49 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 20 through 22
      removed outlier: 3.871A  pdb=" N   ASP L  71 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 115 through 119
      removed outlier: 3.720A  pdb=" N   VAL L 134 " --> pdb=" O   PHE L 119 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   TYR L 174 " --> pdb=" O   ASN L 139 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   GLN L 161 " --> pdb=" O   THR L 179 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 154 through 155
      removed outlier: 3.875A  pdb=" N   LYS L 146 " --> pdb=" O   THR L 198 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR L 198 " --> pdb=" O   LYS L 146 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN L 148 " --> pdb=" O   GLU L 196 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LYS L 208 " --> pdb=" O   CYS L 195 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.811A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   SER A 399 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   ALA A 435 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 453 through 454
      removed outlier: 3.747A  pdb=" N   ARG A 493 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474

    108 hydrogen bonds defined for protein.
    276 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: 0.74

  Time building geometry restraints manager: 0.47 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1552
        1.34 -     1.46: 1239
        1.46 -     1.58: 2144
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 4959
  Sorted by residual:
  bond pdb=" C   SER L  95 "
       pdb=" N   PRO L  96 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 8.70e-03 1.32e+04 4.65e+00
  bond pdb=" C   LYS H 209 "
       pdb=" N   PRO H 210 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.038 2.34e-02 1.83e+03 2.58e+00
  bond pdb=" C   TYR A 489 "
       pdb=" N   PHE A 490 "
    ideal  model  delta    sigma   weight residual
    1.332  1.353 -0.022 1.92e-02 2.71e+03 1.28e+00
  bond pdb=" N   ILE A 410 "
       pdb=" CA  ILE A 410 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.017 1.57e-02 4.06e+03 1.15e+00
  bond pdb=" C   THR L 179 "
       pdb=" N   LEU L 180 "
    ideal  model  delta    sigma   weight residual
    1.331  1.342 -0.012 1.29e-02 6.01e+03 8.63e-01
  ... (remaining 4954 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 6332
        1.15 -     2.30: 313
        2.30 -     3.46: 82
        3.46 -     4.61: 14
        4.61 -     5.76: 10
  Bond angle restraints: 6751
  Sorted by residual:
  angle pdb=" N   TRP H  47 "
        pdb=" CA  TRP H  47 "
        pdb=" C   TRP H  47 "
      ideal   model   delta    sigma   weight residual
     108.45  113.85   -5.40 1.26e+00 6.30e-01 1.84e+01
  angle pdb=" N   ILE A 418 "
        pdb=" CA  ILE A 418 "
        pdb=" C   ILE A 418 "
      ideal   model   delta    sigma   weight residual
     112.29  108.26    4.03 9.40e-01 1.13e+00 1.84e+01
  angle pdb=" N   ASP H  66 "
        pdb=" CA  ASP H  66 "
        pdb=" C   ASP H  66 "
      ideal   model   delta    sigma   weight residual
     114.56  109.22    5.34 1.27e+00 6.20e-01 1.77e+01
  angle pdb=" N   GLU L  82 "
        pdb=" CA  GLU L  82 "
        pdb=" C   GLU L  82 "
      ideal   model   delta    sigma   weight residual
     114.09  108.85    5.24 1.55e+00 4.16e-01 1.14e+01
  angle pdb=" N   SER H 122 "
        pdb=" CA  SER H 122 "
        pdb=" C   SER H 122 "
      ideal   model   delta    sigma   weight residual
     107.73  111.58   -3.85 1.34e+00 5.57e-01 8.27e+00
  ... (remaining 6746 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.00: 2830
       17.00 -    33.99: 100
       33.99 -    50.99: 17
       50.99 -    67.98: 5
       67.98 -    84.98: 3
  Dihedral angle restraints: 2955
    sinusoidal: 1149
      harmonic: 1806
  Sorted by residual:
  dihedral pdb=" CA  GLU L  80 "
           pdb=" C   GLU L  80 "
           pdb=" N   PRO L  81 "
           pdb=" CA  PRO L  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.11  -20.89     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" CA  GLU H 156 "
           pdb=" C   GLU H 156 "
           pdb=" N   PRO H 157 "
           pdb=" CA  PRO H 157 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.22   20.78     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" SG  CYS H 101 "
           pdb=" CB  CYS H 106 "
           pdb=" SG  CYS H 106 "
           pdb=" CA  CYS H 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -73.00    0.62  -73.62     1      2.00e+01 2.50e-03 1.72e+01
  ... (remaining 2952 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 431
       0.026 -    0.051: 176
       0.051 -    0.077: 60
       0.077 -    0.102: 54
       0.102 -    0.128: 20
  Chirality restraints: 741
  Sorted by residual:
  chirality pdb=" CA  ILE L  49 "
            pdb=" N   ILE L  49 "
            pdb=" C   ILE L  49 "
            pdb=" CB  ILE L  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE H  51 "
            pdb=" N   ILE H  51 "
            pdb=" C   ILE H  51 "
            pdb=" CB  ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  VAL H 129 "
            pdb=" N   VAL H 129 "
            pdb=" C   VAL H 129 "
            pdb=" CB  VAL H 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 738 not shown)

  Planarity restraints: 873
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  13 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.50e+00
        pdb=" N   PRO H  14 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 372 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.44e+00
        pdb=" N   PRO A 373 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 373 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 373 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 156 "    0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO H 157 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO H 157 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO H 157 "    0.018 5.00e-02 4.00e+02
  ... (remaining 870 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1606
        2.84 -     3.36: 3821
        3.36 -     3.87: 7271
        3.87 -     4.39: 7869
        4.39 -     4.90: 14182
  Nonbonded interactions: 34749
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU L 196 "
            pdb=" OG1 THR L 207 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" NH1 ARG H  12 "
            pdb=" O   SER H  17 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" OE2 GLU A 340 "
            pdb=" NZ  LYS A 356 "
     model   vdw
     2.373 3.120
  nonbonded pdb=" NZ  LYS H  19 "
            pdb=" OE2 GLU H  82 "
     model   vdw
     2.425 3.120
  nonbonded pdb=" O   PRO H 193 "
            pdb=" OG  SER H 196 "
     model   vdw
     2.430 3.040
  ... (remaining 34744 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 individual isotropic
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:             3.000
  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:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     6.490
  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:7.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
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   0.038   4968  Z= 0.137
  Angle     :  0.638   5.760   6769  Z= 0.393
  Chirality :  0.041   0.128    741
  Planarity :  0.004   0.047    873
  Dihedral  :  8.962  84.975   1774
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  :  6.68 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.30), residues: 616
  helix: -4.63 (0.37), residues: 40
  sheet: -1.63 (0.32), residues: 235
  loop : -3.62 (0.28), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  87 
 TYR   0.007   0.001   TYR L  92 
 PHE   0.005   0.001   PHE L 140 
 TRP   0.007   0.001   TRP H  50 
 HIS   0.001   0.000   HIS H 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4959)
  covalent geometry    : angle       0.63806 ( 6751)
  SS BOND              : bond        0.00166 (    9)
  SS BOND              : angle       0.64861 (   18)
  hydrogen bonds       : bond        0.34139 (  108)
  hydrogen bonds       : angle      10.13452 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.195 
Fit side-chains
REVERT: H    4 LEU cc_start: 0.7747 (mp) cc_final: 0.7456 (mp)
REVERT: H   55 SER cc_start: 0.7961 (t) cc_final: 0.7701 (t)
REVERT: H  117 THR cc_start: 0.7706 (m) cc_final: 0.7447 (p)
REVERT: L   68 SER cc_start: 0.8073 (p) cc_final: 0.7861 (m)
REVERT: L   90 GLN cc_start: 0.8353 (tt0) cc_final: 0.8089 (tt0)
REVERT: L  127 LYS cc_start: 0.8929 (mttt) cc_final: 0.8667 (mttt)
REVERT: L  133 VAL cc_start: 0.8302 (t) cc_final: 0.8017 (m)
REVERT: L  209 SER cc_start: 0.7999 (p) cc_final: 0.7779 (t)
REVERT: A  334 ASN cc_start: 0.6235 (p0) cc_final: 0.5833 (t160)
  outliers start: 15
  outliers final: 1
  residues processed: 140
  average time/residue: 0.3886
  time to fit residues: 56.9645
Evaluate side-chains
  101 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   48 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.2980
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.0670
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
H  62 GLN
H 100 HIS
H 105 ASN
H 107 HIS
H 179 GLN
L   6 GLN
L  39 GLN
L  90 GLN
L 101 GLN
A 414 GLN
** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 481 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.150308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.131071 restraints weight = 7777.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 2.66
r_work: 0.3696 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4968  Z= 0.139
  Angle     :  0.659  11.279   6769  Z= 0.325
  Chirality :  0.045   0.150    741
  Planarity :  0.005   0.046    873
  Dihedral  :  4.243  25.600    684
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 15.77 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.44 (0.31), residues: 616
  helix: -3.97 (0.59), residues: 34
  sheet: -0.71 (0.35), residues: 219
  loop : -3.32 (0.28), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.013   0.001   TYR A 501 
 PHE   0.015   0.001   PHE L 210 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.000   HIS H 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4959)
  covalent geometry    : angle       0.65646 ( 6751)
  SS BOND              : bond        0.00433 (    9)
  SS BOND              : angle       1.30255 (   18)
  hydrogen bonds       : bond        0.04372 (  108)
  hydrogen bonds       : angle       6.27336 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.149 
Fit side-chains
REVERT: H    4 LEU cc_start: 0.8051 (mp) cc_final: 0.7749 (mp)
REVERT: H   55 SER cc_start: 0.8144 (t) cc_final: 0.7896 (t)
REVERT: H  159 THR cc_start: 0.8256 (OUTLIER) cc_final: 0.8049 (p)
REVERT: L   81 PRO cc_start: 0.8304 (Cg_endo) cc_final: 0.8043 (Cg_exo)
REVERT: L   90 GLN cc_start: 0.8462 (tt0) cc_final: 0.8261 (tt0)
REVERT: L  108 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8050 (mtpp)
REVERT: L  109 ARG cc_start: 0.7717 (ttp80) cc_final: 0.7442 (ttp80)
REVERT: L  127 LYS cc_start: 0.8983 (mttt) cc_final: 0.8633 (mttt)
REVERT: L  133 VAL cc_start: 0.8545 (t) cc_final: 0.8273 (m)
REVERT: L  175 SER cc_start: 0.8189 (m) cc_final: 0.7959 (p)
REVERT: L  209 SER cc_start: 0.7966 (p) cc_final: 0.7622 (t)
REVERT: A  334 ASN cc_start: 0.6536 (p0) cc_final: 0.6068 (t160)
  outliers start: 21
  outliers final: 9
  residues processed: 117
  average time/residue: 0.3729
  time to fit residues: 45.8108
Evaluate side-chains
  109 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue  181 THR
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 42 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.3788

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

Flipped N/Q/H residues before XYZ refinement:
H 115 GLN
L  39 GLN
L 167 GLN
A 439 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.149023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.129513 restraints weight = 7686.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3783 rms_B_bonded: 2.65
r_work: 0.3675 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4968  Z= 0.149
  Angle     :  0.673  10.754   6769  Z= 0.333
  Chirality :  0.046   0.175    741
  Planarity :  0.004   0.049    873
  Dihedral  :  4.506  26.187    684
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 17.63 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.32), residues: 616
  helix: -3.57 (0.69), residues: 34
  sheet: -0.24 (0.36), residues: 217
  loop : -3.18 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.012   0.002   TYR H 184 
 PHE   0.016   0.001   PHE A 456 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.001   0.000   HIS H 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4959)
  covalent geometry    : angle       0.66914 ( 6751)
  SS BOND              : bond        0.00426 (    9)
  SS BOND              : angle       1.58294 (   18)
  hydrogen bonds       : bond        0.04185 (  108)
  hydrogen bonds       : angle       5.79783 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.194 
Fit side-chains
REVERT: H   58 THR cc_start: 0.8299 (p) cc_final: 0.8007 (p)
REVERT: L    6 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8126 (mt0)
REVERT: L   90 GLN cc_start: 0.8363 (tt0) cc_final: 0.8116 (tt0)
REVERT: L  108 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8069 (mtpp)
REVERT: L  109 ARG cc_start: 0.7666 (ttp80) cc_final: 0.7431 (ttp80)
REVERT: L  127 LYS cc_start: 0.9003 (mttt) cc_final: 0.8642 (mttt)
REVERT: L  175 SER cc_start: 0.8179 (m) cc_final: 0.7961 (p)
REVERT: L  209 SER cc_start: 0.7847 (p) cc_final: 0.7500 (t)
REVERT: A  358 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7653 (mp)
REVERT: A  386 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6596 (pttt)
  outliers start: 26
  outliers final: 11
  residues processed: 115
  average time/residue: 0.4084
  time to fit residues: 49.1790
Evaluate side-chains
  112 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   16 THR
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0270
   chunk 52 optimal weight:    0.0970
   chunk 22 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0000
   overall best weight:    0.2240

-------------------------------------------------------------------------------
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 = 0.4034 r_free = 0.4034 target = 0.150790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.130872 restraints weight = 7624.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3796 rms_B_bonded: 2.71
r_work: 0.3684 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4968  Z= 0.114
  Angle     :  0.659  10.898   6769  Z= 0.317
  Chirality :  0.045   0.159    741
  Planarity :  0.004   0.048    873
  Dihedral  :  4.425  25.374    684
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 18.74 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.76 (0.32), residues: 616
  helix: -3.36 (0.74), residues: 34
  sheet: -0.09 (0.36), residues: 219
  loop : -2.99 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.009   0.001   TYR A 501 
 PHE   0.015   0.001   PHE L 210 
 TRP   0.012   0.001   TRP L 149 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4959)
  covalent geometry    : angle       0.65681 ( 6751)
  SS BOND              : bond        0.00413 (    9)
  SS BOND              : angle       1.24505 (   18)
  hydrogen bonds       : bond        0.03284 (  108)
  hydrogen bonds       : angle       5.50763 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.199 
Fit side-chains
REVERT: H  132 LEU cc_start: 0.7115 (tm) cc_final: 0.6861 (tt)
REVERT: L    6 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8121 (mt0)
REVERT: L   90 GLN cc_start: 0.8330 (tt0) cc_final: 0.8100 (tt0)
REVERT: L  105 VAL cc_start: 0.8243 (t) cc_final: 0.7973 (m)
REVERT: L  108 LYS cc_start: 0.8425 (ttpp) cc_final: 0.8086 (mtpp)
REVERT: L  109 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7407 (ttp80)
REVERT: L  127 LYS cc_start: 0.9014 (mttt) cc_final: 0.8650 (mttt)
REVERT: L  147 VAL cc_start: 0.9173 (m) cc_final: 0.8871 (p)
REVERT: L  148 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: L  175 SER cc_start: 0.8205 (m) cc_final: 0.7940 (p)
REVERT: L  209 SER cc_start: 0.7765 (p) cc_final: 0.7441 (t)
REVERT: A  334 ASN cc_start: 0.6502 (p0) cc_final: 0.6124 (t160)
REVERT: A  358 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: A  386 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6555 (pttt)
  outliers start: 25
  outliers final: 13
  residues processed: 122
  average time/residue: 0.4643
  time to fit residues: 59.5281
Evaluate side-chains
  115 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   16 THR
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    0.0670
   chunk 56 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 57 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0020
   chunk 35 optimal weight:    0.1980
   chunk 28 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0170
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.0964

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

Flipped N/Q/H residues before XYZ refinement:
A 334 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.152367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.132569 restraints weight = 7750.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3826 rms_B_bonded: 2.69
r_work: 0.3718 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4968  Z= 0.096
  Angle     :  0.634  11.543   6769  Z= 0.299
  Chirality :  0.044   0.146    741
  Planarity :  0.004   0.047    873
  Dihedral  :  4.187  24.364    684
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.71 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.44 (0.33), residues: 616
  helix: -3.27 (0.76), residues: 34
  sheet:  0.15 (0.36), residues: 218
  loop : -2.76 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.006   0.001   TYR L  92 
 PHE   0.016   0.001   PHE A 456 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 4959)
  covalent geometry    : angle       0.63314 ( 6751)
  SS BOND              : bond        0.00312 (    9)
  SS BOND              : angle       0.91788 (   18)
  hydrogen bonds       : bond        0.02682 (  108)
  hydrogen bonds       : angle       5.17560 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.195 
Fit side-chains
REVERT: H   81 MET cc_start: 0.8510 (ttp) cc_final: 0.8281 (ttt)
REVERT: H  132 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6826 (tt)
REVERT: H  201 THR cc_start: 0.3556 (m) cc_final: -0.1099 (t)
REVERT: L   10 THR cc_start: 0.8425 (p) cc_final: 0.8093 (m)
REVERT: L   90 GLN cc_start: 0.8318 (tt0) cc_final: 0.8067 (tt0)
REVERT: L  108 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8104 (mtpp)
REVERT: L  109 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7422 (ttp80)
REVERT: L  127 LYS cc_start: 0.8998 (mttt) cc_final: 0.8642 (mttt)
REVERT: L  147 VAL cc_start: 0.9161 (m) cc_final: 0.8904 (p)
REVERT: L  175 SER cc_start: 0.8179 (m) cc_final: 0.7875 (p)
REVERT: L  209 SER cc_start: 0.7700 (p) cc_final: 0.7390 (t)
REVERT: A  334 ASN cc_start: 0.6340 (p0) cc_final: 0.6005 (t160)
REVERT: A  386 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6218 (mtmt)
  outliers start: 16
  outliers final: 8
  residues processed: 111
  average time/residue: 0.4473
  time to fit residues: 52.2215
Evaluate side-chains
  108 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
L  39 GLN
L 125 GLN
A 481 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.146208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.126613 restraints weight = 7772.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3752 rms_B_bonded: 2.69
r_work: 0.3638 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4968  Z= 0.189
  Angle     :  0.745  11.316   6769  Z= 0.368
  Chirality :  0.047   0.188    741
  Planarity :  0.005   0.050    873
  Dihedral  :  4.935  28.992    684
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.31 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 20.96 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.33), residues: 616
  helix: -3.20 (0.77), residues: 34
  sheet:  0.31 (0.36), residues: 216
  loop : -2.87 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.015   0.002   TYR H 184 
 PHE   0.028   0.002   PHE A 456 
 TRP   0.009   0.002   TRP A 353 
 HIS   0.001   0.000   HIS H 172 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4959)
  covalent geometry    : angle       0.74196 ( 6751)
  SS BOND              : bond        0.00669 (    9)
  SS BOND              : angle       1.51960 (   18)
  hydrogen bonds       : bond        0.04245 (  108)
  hydrogen bonds       : angle       5.38360 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.200 
Fit side-chains
REVERT: H   58 THR cc_start: 0.8435 (p) cc_final: 0.8182 (p)
REVERT: H  132 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6979 (tt)
REVERT: L    6 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8220 (mt0)
REVERT: L   10 THR cc_start: 0.8401 (p) cc_final: 0.8070 (m)
REVERT: L  105 VAL cc_start: 0.8239 (t) cc_final: 0.8012 (m)
REVERT: L  108 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8138 (mtpp)
REVERT: L  109 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7424 (ttp80)
REVERT: L  127 LYS cc_start: 0.9016 (mttt) cc_final: 0.8641 (mttt)
REVERT: L  148 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: L  175 SER cc_start: 0.8270 (m) cc_final: 0.7945 (p)
REVERT: L  209 SER cc_start: 0.7755 (p) cc_final: 0.7446 (t)
REVERT: A  386 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6510 (pttt)
  outliers start: 28
  outliers final: 17
  residues processed: 119
  average time/residue: 0.3963
  time to fit residues: 49.8134
Evaluate side-chains
  118 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0060
   chunk 15 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4594

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.147542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.128043 restraints weight = 7641.518|
|-----------------------------------------------------------------------------|
r_work (start): 0.3757 rms_B_bonded: 2.69
r_work: 0.3643 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4968  Z= 0.170
  Angle     :  0.735  11.497   6769  Z= 0.357
  Chirality :  0.047   0.182    741
  Planarity :  0.005   0.050    873
  Dihedral  :  4.951  28.075    684
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.20 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 21.89 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.42 (0.33), residues: 616
  helix: -3.14 (0.78), residues: 34
  sheet:  0.24 (0.36), residues: 218
  loop : -2.82 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.013   0.002   TYR H 184 
 PHE   0.015   0.001   PHE L 210 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4959)
  covalent geometry    : angle       0.73019 ( 6751)
  SS BOND              : bond        0.00612 (    9)
  SS BOND              : angle       1.79263 (   18)
  hydrogen bonds       : bond        0.03836 (  108)
  hydrogen bonds       : angle       5.36914 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 102
  time to evaluate  : 0.195 
Fit side-chains
REVERT: H   74 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8256 (mtp)
REVERT: H   81 MET cc_start: 0.8458 (ttp) cc_final: 0.8158 (ttt)
REVERT: H  132 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6922 (tt)
REVERT: L    6 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.8077 (mt0)
REVERT: L   10 THR cc_start: 0.8403 (p) cc_final: 0.8051 (m)
REVERT: L  105 VAL cc_start: 0.8251 (t) cc_final: 0.8022 (m)
REVERT: L  108 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8108 (mtpp)
REVERT: L  127 LYS cc_start: 0.9023 (mttt) cc_final: 0.8634 (mttt)
REVERT: L  148 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: L  209 SER cc_start: 0.7748 (p) cc_final: 0.7458 (t)
REVERT: A  386 LYS cc_start: 0.7092 (OUTLIER) cc_final: 0.6604 (pttt)
  outliers start: 29
  outliers final: 19
  residues processed: 117
  average time/residue: 0.4159
  time to fit residues: 51.2802
Evaluate side-chains
  125 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   74 MET
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.0770
   chunk 38 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0980
   chunk 59 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.2136

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.150232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.130500 restraints weight = 7684.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3794 rms_B_bonded: 2.67
r_work: 0.3686 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4968  Z= 0.118
  Angle     :  0.714  11.948   6769  Z= 0.337
  Chirality :  0.045   0.149    741
  Planarity :  0.005   0.051    873
  Dihedral  :  4.679  26.856    684
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.39 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 23.38 %
    Favored  : 71.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.30 (0.33), residues: 616
  helix: -3.00 (0.79), residues: 34
  sheet:  0.26 (0.36), residues: 221
  loop : -2.72 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.011   0.001   TYR A 501 
 PHE   0.013   0.001   PHE L 210 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 4959)
  covalent geometry    : angle       0.71195 ( 6751)
  SS BOND              : bond        0.00492 (    9)
  SS BOND              : angle       1.33129 (   18)
  hydrogen bonds       : bond        0.02930 (  108)
  hydrogen bonds       : angle       5.13197 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.178 
Fit side-chains
REVERT: H   81 MET cc_start: 0.8520 (ttp) cc_final: 0.8234 (ttt)
REVERT: H  132 LEU cc_start: 0.7128 (OUTLIER) cc_final: 0.6825 (tt)
REVERT: L    6 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8118 (mt0)
REVERT: L   10 THR cc_start: 0.8359 (p) cc_final: 0.8043 (m)
REVERT: L   20 THR cc_start: 0.8860 (p) cc_final: 0.8421 (p)
REVERT: L  105 VAL cc_start: 0.8259 (t) cc_final: 0.8055 (m)
REVERT: L  108 LYS cc_start: 0.8469 (ttpp) cc_final: 0.8169 (mtpp)
REVERT: L  148 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: L  209 SER cc_start: 0.7677 (p) cc_final: 0.7472 (t)
REVERT: A  386 LYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6535 (pttt)
  outliers start: 25
  outliers final: 20
  residues processed: 118
  average time/residue: 0.3812
  time to fit residues: 47.6309
Evaluate side-chains
  121 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   68 VAL
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
L 167 GLN
A 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.148107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.128181 restraints weight = 7533.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.72
r_work: 0.3656 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4968  Z= 0.158
  Angle     :  0.760  11.524   6769  Z= 0.362
  Chirality :  0.047   0.172    741
  Planarity :  0.005   0.053    873
  Dihedral  :  4.923  26.891    684
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.69 %
    Favored  : 88.31 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 23.01 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.34 (0.33), residues: 616
  helix: -3.07 (0.78), residues: 34
  sheet:  0.14 (0.35), residues: 233
  loop : -2.76 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.013   0.002   TYR A 501 
 PHE   0.015   0.001   PHE L 210 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4959)
  covalent geometry    : angle       0.75646 ( 6751)
  SS BOND              : bond        0.00592 (    9)
  SS BOND              : angle       1.58894 (   18)
  hydrogen bonds       : bond        0.03609 (  108)
  hydrogen bonds       : angle       5.20066 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 0.203 
Fit side-chains
REVERT: H   81 MET cc_start: 0.8529 (ttp) cc_final: 0.8244 (ttt)
REVERT: H  132 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6864 (tt)
REVERT: L    6 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8107 (mt0)
REVERT: L   76 ILE cc_start: 0.8250 (mm) cc_final: 0.7801 (mm)
REVERT: L  108 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8204 (mtpp)
REVERT: L  209 SER cc_start: 0.7656 (p) cc_final: 0.7447 (t)
REVERT: A  386 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6519 (pttt)
  outliers start: 24
  outliers final: 20
  residues processed: 115
  average time/residue: 0.3942
  time to fit residues: 47.9752
Evaluate side-chains
  119 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 6 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** L 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 167 GLN
A 409 GLN
A 481 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.146593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.127046 restraints weight = 7641.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 2.70
r_work: 0.3638 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4968  Z= 0.180
  Angle     :  0.777  10.821   6769  Z= 0.377
  Chirality :  0.048   0.181    741
  Planarity :  0.005   0.055    873
  Dihedral  :  5.125  27.350    684
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.82 %
    Favored  : 87.18 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 23.19 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.43 (0.33), residues: 616
  helix: -3.12 (0.78), residues: 34
  sheet:  0.04 (0.35), residues: 239
  loop : -2.84 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 408 
 TYR   0.016   0.002   TYR A 501 
 PHE   0.017   0.002   PHE L 210 
 TRP   0.007   0.001   TRP A 353 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 4959)
  covalent geometry    : angle       0.77347 ( 6751)
  SS BOND              : bond        0.00626 (    9)
  SS BOND              : angle       1.66217 (   18)
  hydrogen bonds       : bond        0.03966 (  108)
  hydrogen bonds       : angle       5.24228 (  276)

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.163 
Fit side-chains
REVERT: H   74 MET cc_start: 0.8550 (mtm) cc_final: 0.8324 (mtp)
REVERT: H   81 MET cc_start: 0.8493 (ttp) cc_final: 0.8217 (ttt)
REVERT: H  132 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6935 (tt)
REVERT: L    6 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8112 (mt0)
REVERT: L   10 THR cc_start: 0.8157 (p) cc_final: 0.7918 (t)
REVERT: L   76 ILE cc_start: 0.8253 (mm) cc_final: 0.7794 (mm)
REVERT: L  108 LYS cc_start: 0.8454 (ttpp) cc_final: 0.8156 (mtpp)
REVERT: L  209 SER cc_start: 0.7722 (p) cc_final: 0.7505 (t)
REVERT: A  386 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6580 (pttt)
  outliers start: 23
  outliers final: 20
  residues processed: 113
  average time/residue: 0.3879
  time to fit residues: 46.2778
Evaluate side-chains
  120 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   32 SER
Chi-restraints excluded: chain H residue   48 ILE
Chi-restraints excluded: chain H residue   52 VAL
Chi-restraints excluded: chain H residue   76 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  112 ILE
Chi-restraints excluded: chain H residue  115 GLN
Chi-restraints excluded: chain H residue  132 LEU
Chi-restraints excluded: chain H residue  143 THR
Chi-restraints excluded: chain H residue  146 LEU
Chi-restraints excluded: chain H residue  159 THR
Chi-restraints excluded: chain L residue    6 GLN
Chi-restraints excluded: chain L residue   21 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  116 VAL
Chi-restraints excluded: chain L residue  133 VAL
Chi-restraints excluded: chain L residue  162 GLU
Chi-restraints excluded: chain L residue  164 VAL
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  386 LYS
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  483 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 29 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0060
   chunk 13 optimal weight:    0.0970
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.2994

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
A 481 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.148298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.128495 restraints weight = 7637.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3769 rms_B_bonded: 2.72
r_work: 0.3660 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7433
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4968  Z= 0.139
  Angle     :  0.760  11.549   6769  Z= 0.364
  Chirality :  0.046   0.165    741
  Planarity :  0.005   0.056    873
  Dihedral  :  4.930  26.951    684
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 23.75 %
    Favored  : 72.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.33), residues: 616
  helix: -3.06 (0.80), residues: 34
  sheet:  0.11 (0.35), residues: 237
  loop : -2.76 (0.31), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 408 
 TYR   0.017   0.001   TYR A 501 
 PHE   0.016   0.001   PHE L 210 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4959)
  covalent geometry    : angle       0.75807 ( 6751)
  SS BOND              : bond        0.00532 (    9)
  SS BOND              : angle       1.39538 (   18)
  hydrogen bonds       : bond        0.03309 (  108)
  hydrogen bonds       : angle       5.07787 (  276)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1824.29 seconds
wall clock time: 31 minutes 50.91 seconds (1910.91 seconds total)