Starting phenix.real_space_refine
on Tue Feb  3 16:40:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kwf_62609/02_2026/9kwf_62609.cif"
  }
  resolution = 3.52
  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=   1.000
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      26      5.16       5
     C    3160      2.51       5
     N     840      2.21       5
     O     942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4968
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 324, 2484
          Classifications: {'peptide': 324}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 15, 'TRANS': 308}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'TRP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Restraints were copied for chains:
    A
  Time building chain proxies: 1.63, per 1000 atoms: 0.33
  Number of scatterers: 4968
  At special positions: 0
  Unit cell: (111.556, 79.492, 61.456, 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      26     16.00
     O     942      8.00
     N     840      7.00
     C    3160      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: 0.37
  Conformation dependent library (CDL) restraints added in 386.4 milliseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      38.1% alpha, 9.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'B' and resid 7 through 21
      removed outlier: 4.030A  pdb=" N   GLU B  11 " --> pdb=" O   THR B   7 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ASN B  12 " --> pdb=" O   SER B   8 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   GLY B  16 " --> pdb=" O   ASN B  12 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA B  19 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 43
      removed outlier: 4.461A  pdb=" N   THR B  43 " --> pdb=" O   THR B  40 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 40 through 43'
    Processing helix  chain 'B' and resid 44 through 57
      removed outlier: 3.924A  pdb=" N   VAL B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 77
      removed outlier: 3.812A  pdb=" N   GLU B  75 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 110 through 114
    Processing helix  chain 'B' and resid 121 through 125
      removed outlier: 4.062A  pdb=" N   MET B 124 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
      removed outlier: 3.528A  pdb=" N   LEU B 130 " --> pdb=" O   GLY B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 161
    Processing helix  chain 'B' and resid 179 through 192
      removed outlier: 3.541A  pdb=" N   LEU B 183 " --> pdb=" O   ALA B 179 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   SER B 184 " --> pdb=" O   ILE B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 206
    Processing helix  chain 'B' and resid 221 through 231
    Processing helix  chain 'B' and resid 245 through 256
      removed outlier: 3.756A  pdb=" N   ALA B 250 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ILE B 251 " --> pdb=" O   TYR B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 393
    Processing helix  chain 'B' and resid 404 through 408
    Processing helix  chain 'A' and resid 8 through 21
      removed outlier: 3.619A  pdb=" N   ASN A  12 " --> pdb=" O   SER A   8 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   GLY A  16 " --> pdb=" O   ASN A  12 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   MET A  17 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   ALA A  19 " --> pdb=" O   GLU A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 43
      removed outlier: 4.461A  pdb=" N   THR A  43 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 40 through 43'
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.923A  pdb=" N   VAL A  48 " --> pdb=" O   THR A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 3.813A  pdb=" N   GLU A  75 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 114
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 4.063A  pdb=" N   MET A 124 " --> pdb=" O   GLU A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
      removed outlier: 3.528A  pdb=" N   LEU A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 161
    Processing helix  chain 'A' and resid 179 through 192
      removed outlier: 3.541A  pdb=" N   LEU A 183 " --> pdb=" O   ALA A 179 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   SER A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 206
    Processing helix  chain 'A' and resid 221 through 231
    Processing helix  chain 'A' and resid 245 through 256
      removed outlier: 3.756A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ILE A 251 " --> pdb=" O   TYR A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 404 through 408
    Processing sheet with id=AA1, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.523A  pdb=" N   ALA B  84 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA B  61 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL B 117 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 236 through 238
      removed outlier: 5.452A  pdb=" N   ILE B 236 " --> pdb=" O   MET B 387 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 268 through 270
    Processing sheet with id=AA4, first strand: chain 'B' and resid 309 through 313
      removed outlier: 3.624A  pdb=" N   LEU B 321 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   VAL B 311 " --> pdb=" O   TRP B 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 403
      removed outlier: 3.602A  pdb=" N   ALA B 431 " --> pdb=" O   VAL B 400 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.523A  pdb=" N   ALA A  84 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   ALA A  61 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL A 117 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 238
      removed outlier: 5.452A  pdb=" N   ILE A 236 " --> pdb=" O   MET A 387 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 268 through 270
    Processing sheet with id=AA9, first strand: chain 'A' and resid 309 through 313
      removed outlier: 3.623A  pdb=" N   LEU A 321 " --> pdb=" O   ALA A 309 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   VAL A 311 " --> pdb=" O   TRP A 319 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 403
      removed outlier: 3.602A  pdb=" N   ALA A 431 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)

    134 hydrogen bonds defined for protein.
    354 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: 0.64

  Time building geometry restraints manager: 0.51 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: 1612
        1.34 -     1.46: 925
        1.46 -     1.58: 2483
        1.58 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 5058
  Sorted by residual:
  bond pdb=" C   ARG A 136 "
       pdb=" N   PRO A 137 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.32e+00
  bond pdb=" C   ARG B 136 "
       pdb=" N   PRO B 137 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.31e+00
  bond pdb=" C   ALA B 314 "
       pdb=" O   ALA B 314 "
    ideal  model  delta    sigma   weight residual
    1.242  1.231  0.010 1.00e-02 1.00e+04 1.05e+00
  bond pdb=" CA  ALA A 314 "
       pdb=" C   ALA A 314 "
    ideal  model  delta    sigma   weight residual
    1.528  1.519  0.009 8.80e-03 1.29e+04 1.05e+00
  bond pdb=" CA  ALA B 314 "
       pdb=" C   ALA B 314 "
    ideal  model  delta    sigma   weight residual
    1.528  1.519  0.009 8.80e-03 1.29e+04 9.77e-01
  ... (remaining 5053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 6712
        1.86 -     3.73: 118
        3.73 -     5.59: 30
        5.59 -     7.46: 4
        7.46 -     9.32: 4
  Bond angle restraints: 6868
  Sorted by residual:
  angle pdb=" C   ALA B 314 "
        pdb=" CA  ALA B 314 "
        pdb=" CB  ALA B 314 "
      ideal   model   delta    sigma   weight residual
     116.63  111.24    5.39 1.16e+00 7.43e-01 2.16e+01
  angle pdb=" C   ALA A 314 "
        pdb=" CA  ALA A 314 "
        pdb=" CB  ALA A 314 "
      ideal   model   delta    sigma   weight residual
     116.63  111.27    5.36 1.16e+00 7.43e-01 2.13e+01
  angle pdb=" CA  ALA A 314 "
        pdb=" C   ALA A 314 "
        pdb=" N   SER A 315 "
      ideal   model   delta    sigma   weight residual
     119.63  116.41    3.22 8.10e-01 1.52e+00 1.58e+01
  angle pdb=" CA  ALA B 314 "
        pdb=" C   ALA B 314 "
        pdb=" N   SER B 315 "
      ideal   model   delta    sigma   weight residual
     119.63  116.46    3.17 8.10e-01 1.52e+00 1.53e+01
  angle pdb=" N   GLU A 317 "
        pdb=" CA  GLU A 317 "
        pdb=" C   GLU A 317 "
      ideal   model   delta    sigma   weight residual
     107.99  113.86   -5.87 1.76e+00 3.23e-01 1.11e+01
  ... (remaining 6863 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 2510
       16.16 -    32.31: 370
       32.31 -    48.47: 124
       48.47 -    64.63: 22
       64.63 -    80.78: 6
  Dihedral angle restraints: 3032
    sinusoidal: 1164
      harmonic: 1868
  Sorted by residual:
  dihedral pdb=" CA  GLY A  16 "
           pdb=" C   GLY A  16 "
           pdb=" N   MET A  17 "
           pdb=" CA  MET A  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.46   17.54     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  GLY B  16 "
           pdb=" C   GLY B  16 "
           pdb=" N   MET B  17 "
           pdb=" CA  MET B  17 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.47   17.53     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  LEU B 419 "
           pdb=" C   LEU B 419 "
           pdb=" N   TYR B 420 "
           pdb=" CA  TYR B 420 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.29   16.71     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 3029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 433
       0.025 -    0.049: 203
       0.049 -    0.074: 107
       0.074 -    0.098: 42
       0.098 -    0.122: 33
  Chirality restraints: 818
  Sorted by residual:
  chirality pdb=" CA  ILE A 270 "
            pdb=" N   ILE A 270 "
            pdb=" C   ILE A 270 "
            pdb=" CB  ILE A 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.75e-01
  chirality pdb=" CA  ILE B 270 "
            pdb=" N   ILE B 270 "
            pdb=" C   ILE B 270 "
            pdb=" CB  ILE B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality pdb=" CA  ILE A 432 "
            pdb=" N   ILE A 432 "
            pdb=" C   ILE A 432 "
            pdb=" CB  ILE A 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  ... (remaining 815 not shown)

  Planarity restraints: 864
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  16 "    0.010 2.00e-02 2.50e+03   2.06e-02 4.26e+00
        pdb=" C   GLY B  16 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLY B  16 "    0.013 2.00e-02 2.50e+03
        pdb=" N   MET B  17 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  16 "   -0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   GLY A  16 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLY A  16 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   MET A  17 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 261 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.12e+00
        pdb=" N   PRO A 262 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 262 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 262 "    0.025 5.00e-02 4.00e+02
  ... (remaining 861 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 764
        2.76 -     3.29: 4800
        3.29 -     3.83: 7743
        3.83 -     4.36: 9058
        4.36 -     4.90: 15524
  Nonbonded interactions: 37889
  Sorted by model distance:
  nonbonded pdb=" O   ASN B  67 "
            pdb=" OG  SER B  71 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" O   ASN A  67 "
            pdb=" OG  SER A  71 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   PRO B 145 "
            pdb=" NH2 ARG B 417 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" O   PRO A 145 "
            pdb=" NH2 ARG A 417 "
     model   vdw
     2.334 3.120
  nonbonded pdb=" N   GLU B 121 "
            pdb=" OE1 GLU B 121 "
     model   vdw
     2.349 3.120
  ... (remaining 37884 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             18.170
  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:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.220
  Find NCS groups from input model:        0.030
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
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      :  0.003   0.030   5058  Z= 0.139
  Angle     :  0.677   9.323   6868  Z= 0.370
  Chirality :  0.042   0.122    818
  Planarity :  0.004   0.044    864
  Dihedral  : 17.514  80.784   1812
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 33.33 %
    Favored  : 66.30 %
  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 are not related in a simple way.
  whole: -1.84 (0.34), residues: 620
  helix: -0.55 (0.37), residues: 210
  sheet: -0.62 (0.57), residues: 84
  loop : -1.86 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 428 
 TYR   0.011   0.001   TYR B 397 
 PHE   0.005   0.001   PHE A  20 
 TRP   0.014   0.001   TRP B 404 
 HIS   0.002   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5058)
  covalent geometry    : angle       0.67721 ( 6868)
  hydrogen bonds       : bond        0.18947 (  134)
  hydrogen bonds       : angle       7.24276 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  307 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6150 (t80)
REVERT: A  397 TYR cc_start: 0.6347 (m-80) cc_final: 0.6012 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 65
  average time/residue: 0.0511
  time to fit residues: 4.3188
Evaluate side-chains
  57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  307 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0050
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0050
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.3066

-------------------------------------------------------------------------------
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 = 0.4028 r_free = 0.4028 target = 0.153303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.136236 restraints weight = 7795.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.139217 restraints weight = 4954.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.141315 restraints weight = 3502.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.142720 restraints weight = 2651.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.143829 restraints weight = 2140.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7070
moved from start:          0.0823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5058  Z= 0.109
  Angle     :  0.561   6.153   6868  Z= 0.292
  Chirality :  0.041   0.125    818
  Planarity :  0.004   0.043    864
  Dihedral  :  5.019  34.852    683
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 31.50 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.34), residues: 620
  helix: -0.34 (0.37), residues: 212
  sheet: -0.50 (0.63), residues: 68
  loop : -1.78 (0.35), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 313 
 TYR   0.008   0.001   TYR A 397 
 PHE   0.006   0.001   PHE B 307 
 TRP   0.007   0.001   TRP B 404 
 HIS   0.002   0.000   HIS A 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5058)
  covalent geometry    : angle       0.56079 ( 6868)
  hydrogen bonds       : bond        0.03755 (  134)
  hydrogen bonds       : angle       5.67694 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7923 (t80)
REVERT: B  311 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6424 (m)
REVERT: B  319 TRP cc_start: 0.6728 (m100) cc_final: 0.6479 (m100)
REVERT: A   20 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7926 (t80)
REVERT: A  307 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6061 (t80)
REVERT: A  311 VAL cc_start: 0.6694 (OUTLIER) cc_final: 0.6452 (m)
REVERT: A  319 TRP cc_start: 0.6706 (m100) cc_final: 0.6452 (m100)
REVERT: A  397 TYR cc_start: 0.6303 (m-80) cc_final: 0.6087 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 71
  average time/residue: 0.0399
  time to fit residues: 3.9901
Evaluate side-chains
  68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain B residue  390 HIS
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue  129 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  390 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 3 optimal weight:    0.0870
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.4018 r_free = 0.4018 target = 0.152256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.135365 restraints weight = 7741.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.138309 restraints weight = 4935.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.140375 restraints weight = 3488.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.141847 restraints weight = 2655.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.142952 restraints weight = 2131.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.1020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5058  Z= 0.115
  Angle     :  0.552   6.177   6868  Z= 0.287
  Chirality :  0.041   0.123    818
  Planarity :  0.004   0.043    864
  Dihedral  :  4.595  26.552    681
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  7.14 %
    Allowed  : 29.85 %
    Favored  : 63.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.60 (0.34), residues: 620
  helix: -0.15 (0.38), residues: 206
  sheet: -0.90 (0.55), residues: 84
  loop : -1.72 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.011   0.001   TYR B 397 
 PHE   0.005   0.001   PHE A  20 
 TRP   0.005   0.001   TRP B 319 
 HIS   0.002   0.000   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 5058)
  covalent geometry    : angle       0.55187 ( 6868)
  hydrogen bonds       : bond        0.03484 (  134)
  hydrogen bonds       : angle       5.40217 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 55
  time to evaluate  : 0.121 
Fit side-chains
REVERT: B   20 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7997 (t80)
REVERT: B  147 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7250 (mt0)
REVERT: B  311 VAL cc_start: 0.6756 (OUTLIER) cc_final: 0.6520 (m)
REVERT: B  319 TRP cc_start: 0.6767 (m100) cc_final: 0.6530 (m100)
REVERT: A   20 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7997 (t80)
REVERT: A  147 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7317 (mt0)
REVERT: A  307 PHE cc_start: 0.6961 (OUTLIER) cc_final: 0.6073 (t80)
REVERT: A  311 VAL cc_start: 0.6778 (OUTLIER) cc_final: 0.6529 (m)
REVERT: A  319 TRP cc_start: 0.6774 (m100) cc_final: 0.6520 (m100)
  outliers start: 39
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0344
  time to fit residues: 4.1111
Evaluate side-chains
  77 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 54
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0370
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
B 152 ASN
A  67 ASN
A 152 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.150601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.133460 restraints weight = 7737.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.136376 restraints weight = 4954.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.138379 restraints weight = 3530.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.139869 restraints weight = 2703.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.140891 restraints weight = 2175.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7132
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5058  Z= 0.131
  Angle     :  0.578   7.499   6868  Z= 0.301
  Chirality :  0.042   0.124    818
  Planarity :  0.004   0.043    864
  Dihedral  :  4.704  27.993    681
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 29.49 %
    Favored  : 63.55 %
  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 are not related in a simple way.
  whole: -1.74 (0.34), residues: 620
  helix: -0.15 (0.38), residues: 206
  sheet: -1.27 (0.52), residues: 94
  loop : -1.80 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.009   0.001   TYR B 397 
 PHE   0.005   0.001   PHE A  20 
 TRP   0.005   0.001   TRP B 319 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5058)
  covalent geometry    : angle       0.57784 ( 6868)
  hydrogen bonds       : bond        0.03363 (  134)
  hydrogen bonds       : angle       5.26458 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 54
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
REVERT: B   20 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.8024 (t80)
REVERT: B  147 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7296 (mt0)
REVERT: B  311 VAL cc_start: 0.6778 (OUTLIER) cc_final: 0.6558 (m)
REVERT: B  319 TRP cc_start: 0.6794 (m100) cc_final: 0.6533 (m100)
REVERT: A   20 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.8031 (t80)
REVERT: A  147 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7365 (mt0)
REVERT: A  307 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6117 (t80)
REVERT: A  311 VAL cc_start: 0.6768 (OUTLIER) cc_final: 0.6535 (m)
REVERT: A  319 TRP cc_start: 0.6800 (m100) cc_final: 0.6548 (m100)
  outliers start: 38
  outliers final: 24
  residues processed: 86
  average time/residue: 0.0321
  time to fit residues: 4.0620
Evaluate side-chains
  84 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 53
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 PHE
Chi-restraints excluded: chain B residue   29 TRP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  311 VAL
Chi-restraints excluded: chain A residue   20 PHE
Chi-restraints excluded: chain A residue   29 TRP
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  311 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.149651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.132160 restraints weight = 7850.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.135048 restraints weight = 5051.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.137112 restraints weight = 3619.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.138548 restraints weight = 2774.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.139465 restraints weight = 2251.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5058  Z= 0.141
  Angle     :  0.611   7.520   6868  Z= 0.312
  Chirality :  0.043   0.130    818
  Planarity :  0.004   0.042    864
  Dihedral  :  4.815  28.063    681
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 28.94 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.34), residues: 620
  helix: -0.20 (0.38), residues: 206
  sheet: -1.24 (0.53), residues: 94
  loop : -1.85 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 310 
 TYR   0.026   0.002   TYR B 397 
 PHE   0.005   0.001   PHE A  20 
 TRP   0.004   0.001   TRP B 319 
 HIS   0.002   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 5058)
  covalent geometry    : angle       0.61129 ( 6868)
  hydrogen bonds       : bond        0.03421 (  134)
  hydrogen bonds       : angle       5.25563 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 56
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7373 (mt0)
REVERT: B  319 TRP cc_start: 0.6747 (m100) cc_final: 0.6457 (m100)
REVERT: A  147 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7383 (mt0)
REVERT: A  307 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6281 (t80)
REVERT: A  319 TRP cc_start: 0.6791 (m100) cc_final: 0.6516 (m100)
  outliers start: 42
  outliers final: 26
  residues processed: 91
  average time/residue: 0.0428
  time to fit residues: 5.8402
Evaluate side-chains
  82 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 53
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TRP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue   29 TRP
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0980
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    0.1980
   chunk 1 optimal weight:    0.1980
   chunk 13 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4015 r_free = 0.4015 target = 0.151267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.134013 restraints weight = 7843.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.136904 restraints weight = 5014.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.138925 restraints weight = 3565.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.140423 restraints weight = 2728.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.141445 restraints weight = 2197.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5058  Z= 0.123
  Angle     :  0.599   7.940   6868  Z= 0.307
  Chirality :  0.042   0.124    818
  Planarity :  0.004   0.042    864
  Dihedral  :  4.716  23.440    681
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 30.40 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.34), residues: 620
  helix: -0.01 (0.38), residues: 206
  sheet: -1.03 (0.56), residues: 84
  loop : -1.86 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.021   0.001   TYR A 397 
 PHE   0.007   0.001   PHE B  20 
 TRP   0.006   0.001   TRP B 319 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5058)
  covalent geometry    : angle       0.59914 ( 6868)
  hydrogen bonds       : bond        0.03109 (  134)
  hydrogen bonds       : angle       5.21470 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 61
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B  147 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7339 (mt0)
REVERT: B  319 TRP cc_start: 0.6692 (m100) cc_final: 0.6389 (m100)
REVERT: A  147 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7382 (mt0)
REVERT: A  307 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6294 (t80)
REVERT: A  319 TRP cc_start: 0.6674 (m100) cc_final: 0.6390 (m100)
  outliers start: 34
  outliers final: 28
  residues processed: 91
  average time/residue: 0.0418
  time to fit residues: 5.6006
Evaluate side-chains
  86 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 55
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TRP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue   29 TRP
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0050
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6396

-------------------------------------------------------------------------------
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 = 0.3991 r_free = 0.3991 target = 0.149494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.132298 restraints weight = 7830.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.135220 restraints weight = 4987.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.137268 restraints weight = 3532.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.138669 restraints weight = 2685.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.139708 restraints weight = 2176.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.1511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5058  Z= 0.140
  Angle     :  0.615   7.654   6868  Z= 0.316
  Chirality :  0.042   0.130    818
  Planarity :  0.004   0.042    864
  Dihedral  :  4.721  17.006    680
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  7.88 %
    Allowed  : 28.75 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.74 (0.34), residues: 620
  helix: -0.08 (0.37), residues: 206
  sheet: -1.08 (0.56), residues: 84
  loop : -1.92 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 408 
 TYR   0.021   0.002   TYR A 397 
 PHE   0.006   0.001   PHE B  20 
 TRP   0.004   0.001   TRP A  29 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 5058)
  covalent geometry    : angle       0.61464 ( 6868)
  hydrogen bonds       : bond        0.03263 (  134)
  hydrogen bonds       : angle       5.32356 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 58
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
REVERT: B  147 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7309 (mt0)
REVERT: A  147 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7403 (mt0)
REVERT: A  307 PHE cc_start: 0.7064 (OUTLIER) cc_final: 0.6372 (t80)
  outliers start: 43
  outliers final: 33
  residues processed: 91
  average time/residue: 0.0349
  time to fit residues: 4.6580
Evaluate side-chains
  93 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 57
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 TRP
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 TYR
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain A residue   29 TRP
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0980
   chunk 10 optimal weight:    0.0970
   chunk 30 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0000
   chunk 53 optimal weight:    0.0020
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.1390

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.156177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.139152 restraints weight = 7828.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.142096 restraints weight = 5004.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.144210 restraints weight = 3549.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.145645 restraints weight = 2697.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.146801 restraints weight = 2177.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5058  Z= 0.100
  Angle     :  0.561   7.161   6868  Z= 0.288
  Chirality :  0.041   0.128    818
  Planarity :  0.004   0.042    864
  Dihedral  :  4.272  15.472    680
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 30.95 %
    Favored  : 63.92 %
  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 are not related in a simple way.
  whole: -1.48 (0.34), residues: 620
  helix:  0.21 (0.39), residues: 206
  sheet: -0.54 (0.66), residues: 68
  loop : -1.89 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 408 
 TYR   0.012   0.001   TYR A 397 
 PHE   0.005   0.001   PHE B  20 
 TRP   0.006   0.001   TRP B 166 
 HIS   0.002   0.000   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 5058)
  covalent geometry    : angle       0.56105 ( 6868)
  hydrogen bonds       : bond        0.02628 (  134)
  hydrogen bonds       : angle       5.07785 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 64
  time to evaluate  : 0.118 
Fit side-chains
REVERT: B  147 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7253 (mt0)
REVERT: A  121 GLU cc_start: 0.7049 (mp0) cc_final: 0.6695 (mp0)
REVERT: A  147 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7344 (mt0)
REVERT: A  307 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6324 (t80)
  outliers start: 28
  outliers final: 18
  residues processed: 89
  average time/residue: 0.0318
  time to fit residues: 4.2141
Evaluate side-chains
  79 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0670
   chunk 49 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0670
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.152032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.134719 restraints weight = 7916.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137605 restraints weight = 5085.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.139613 restraints weight = 3638.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.141089 restraints weight = 2813.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.142040 restraints weight = 2277.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7118
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5058  Z= 0.129
  Angle     :  0.605   7.338   6868  Z= 0.310
  Chirality :  0.042   0.125    818
  Planarity :  0.004   0.041    864
  Dihedral  :  4.521  16.334    680
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 31.32 %
    Favored  : 64.29 %
  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 are not related in a simple way.
  whole: -1.53 (0.34), residues: 620
  helix:  0.14 (0.38), residues: 206
  sheet: -0.91 (0.57), residues: 84
  loop : -1.85 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.018   0.001   TYR A 397 
 PHE   0.007   0.001   PHE B  20 
 TRP   0.005   0.001   TRP A 404 
 HIS   0.002   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5058)
  covalent geometry    : angle       0.60457 ( 6868)
  hydrogen bonds       : bond        0.02890 (  134)
  hydrogen bonds       : angle       5.24916 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.196 
Fit side-chains
REVERT: B  147 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7192 (mt0)
REVERT: A  121 GLU cc_start: 0.7061 (mp0) cc_final: 0.6699 (mp0)
REVERT: A  147 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7352 (mt0)
REVERT: A  307 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6398 (t80)
  outliers start: 24
  outliers final: 21
  residues processed: 81
  average time/residue: 0.0442
  time to fit residues: 5.3341
Evaluate side-chains
  82 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 58
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0970
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4017 r_free = 0.4017 target = 0.151403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.134037 restraints weight = 7902.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.136939 restraints weight = 5097.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.138952 restraints weight = 3652.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.140441 restraints weight = 2815.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.141356 restraints weight = 2278.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5058  Z= 0.129
  Angle     :  0.618   7.539   6868  Z= 0.317
  Chirality :  0.042   0.128    818
  Planarity :  0.004   0.041    864
  Dihedral  :  4.637  16.672    680
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 31.50 %
    Favored  : 63.74 %
  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 are not related in a simple way.
  whole: -1.50 (0.34), residues: 620
  helix:  0.15 (0.38), residues: 206
  sheet: -0.90 (0.58), residues: 84
  loop : -1.81 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 310 
 TYR   0.015   0.001   TYR B 397 
 PHE   0.005   0.001   PHE B  20 
 TRP   0.004   0.001   TRP A 404 
 HIS   0.002   0.001   HIS B  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5058)
  covalent geometry    : angle       0.61759 ( 6868)
  hydrogen bonds       : bond        0.02991 (  134)
  hydrogen bonds       : angle       5.30421 (  354)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.193 
Fit side-chains
REVERT: B  147 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7234 (mt0)
REVERT: A  121 GLU cc_start: 0.7038 (mp0) cc_final: 0.6710 (mp0)
REVERT: A  147 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7236 (mt0)
REVERT: A  307 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6457 (t80)
  outliers start: 26
  outliers final: 22
  residues processed: 79
  average time/residue: 0.0421
  time to fit residues: 5.0115
Evaluate side-chains
  82 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 THR
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  130 LEU
Chi-restraints excluded: chain B residue  147 GLN
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 SER
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  271 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   85 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain A residue  147 GLN
Chi-restraints excluded: chain A residue  151 VAL
Chi-restraints excluded: chain A residue  156 SER
Chi-restraints excluded: chain A residue  158 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  167 SER
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  271 VAL
Chi-restraints excluded: chain A residue  307 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   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 = 0.3991 r_free = 0.3991 target = 0.148992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.131524 restraints weight = 8048.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.134468 restraints weight = 5168.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.136504 restraints weight = 3680.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.137993 restraints weight = 2825.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138914 restraints weight = 2283.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5058  Z= 0.150
  Angle     :  0.642   7.687   6868  Z= 0.329
  Chirality :  0.043   0.126    818
  Planarity :  0.004   0.041    864
  Dihedral  :  4.815  16.866    680
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.87 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 31.14 %
    Favored  : 63.74 %
  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 are not related in a simple way.
  whole: -1.58 (0.34), residues: 620
  helix:  0.09 (0.38), residues: 206
  sheet: -1.36 (0.53), residues: 94
  loop : -1.72 (0.35), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 310 
 TYR   0.016   0.002   TYR A 397 
 PHE   0.005   0.001   PHE B  20 
 TRP   0.007   0.001   TRP A  29 
 HIS   0.002   0.001   HIS A  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5058)
  covalent geometry    : angle       0.64198 ( 6868)
  hydrogen bonds       : bond        0.03295 (  134)
  hydrogen bonds       : angle       5.30359 (  354)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1019.56 seconds
wall clock time: 18 minutes 22.93 seconds (1102.93 seconds total)