Starting phenix.real_space_refine
on Sat Aug 23 12:23:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ap8_15561/08_2025/8ap8_15561.cif"
  }
  resolution = 3.7
  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=  -0.001 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    3750      2.51       5
     N    1064      2.21       5
     O    1160      1.98       5
     H    6098      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12083
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "M"
      Number of atoms: 768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 768
          Classifications: {'peptide': 48}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 44}
    Chain: "h"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 137, 2158
          Classifications: {'peptide': 137}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 132}
    Chain: "g"
      Number of atoms: 3953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 3953
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 8, 'TRANS': 259}
    Chain: "c"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 44, 741
          Classifications: {'peptide': 44}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 43}
    Chain: "d"
      Number of atoms: 4463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 4463
          Classifications: {'peptide': 270}
          Link IDs: {'PTRANS': 15, 'TRANS': 254}
          Chain breaks: 1
  Time building chain proxies: 2.82, per 1000 atoms: 0.23
  Number of scatterers: 12083
  At special positions: 0
  Unit cell: (117.86, 87.15, 114.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      11     16.00
     O    1160      8.00
     N    1064      7.00
     C    3750      6.00
     H    6098      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 564.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      68.4% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'M' and resid 230 through 236
      removed outlier: 3.564A  pdb=" N   LEU M 236 " --> pdb=" O   GLU M 232 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 236 through 254
    Processing helix  chain 'h' and resid 22 through 32
    Processing helix  chain 'h' and resid 44 through 52
    Processing helix  chain 'h' and resid 55 through 65
      removed outlier: 3.560A  pdb=" N   LYS h  65 " --> pdb=" O   SER h  61 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 68 through 85
    Processing helix  chain 'h' and resid 88 through 96
    Processing helix  chain 'h' and resid 97 through 99
      No H-bonds generated for 'chain 'h' and resid 97 through 99'
    Processing helix  chain 'h' and resid 102 through 123
    Processing helix  chain 'h' and resid 124 through 139
    Processing helix  chain 'h' and resid 141 through 157
    Processing helix  chain 'g' and resid 13 through 29
    Processing helix  chain 'g' and resid 68 through 72
      removed outlier: 3.542A  pdb=" N   SER g  72 " --> pdb=" O   PRO g  69 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 92 through 104
      removed outlier: 4.601A  pdb=" N   ASP g  98 " --> pdb=" O   ARG g  94 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ALA g 101 " --> pdb=" O   LEU g  97 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER g 102 " --> pdb=" O   ASP g  98 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 107 through 133
    Processing helix  chain 'g' and resid 149 through 166
      removed outlier: 3.565A  pdb=" N   GLU g 160 " --> pdb=" O   LYS g 156 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 174 through 184
    Processing helix  chain 'g' and resid 185 through 188
    Processing helix  chain 'g' and resid 196 through 210
    Processing helix  chain 'g' and resid 230 through 246
    Processing helix  chain 'g' and resid 247 through 261
      removed outlier: 3.666A  pdb=" N   ALA g 251 " --> pdb=" O   LEU g 247 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 264 through 269
    Processing helix  chain 'c' and resid 72 through 91
      removed outlier: 3.865A  pdb=" N   THR c  91 " --> pdb=" O   VAL c  87 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 100 through 112
      removed outlier: 3.959A  pdb=" N   VAL c 104 " --> pdb=" O   ASP c 100 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 35 through 56
    Processing helix  chain 'd' and resid 69 through 85
    Processing helix  chain 'd' and resid 86 through 88
      No H-bonds generated for 'chain 'd' and resid 86 through 88'
    Processing helix  chain 'd' and resid 98 through 119
      removed outlier: 3.792A  pdb=" N   ALA d 110 " --> pdb=" O   CYS d 106 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU d 117 " --> pdb=" O   SER d 113 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 125 through 130
    Processing helix  chain 'd' and resid 133 through 164
    Processing helix  chain 'd' and resid 174 through 182
      removed outlier: 3.562A  pdb=" N   SER d 180 " --> pdb=" O   PRO d 176 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 184 through 200
      removed outlier: 4.473A  pdb=" N   VAL d 188 " --> pdb=" O   ASP d 184 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 206 through 218
      removed outlier: 3.503A  pdb=" N   ILE d 210 " --> pdb=" O   ASP d 206 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 219 through 250
      Proline residue:  d 238  - end of helix
    Processing helix  chain 'd' and resid 291 through 295
    Processing helix  chain 'd' and resid 301 through 324
      removed outlier: 3.589A  pdb=" N   ASN d 324 " --> pdb=" O   ALA d 320 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'M' and resid 226 through 227
      removed outlier: 4.553A  pdb=" N   VAL M 226 " --> pdb=" O   ARG d 172 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'g' and resid 32 through 37
      removed outlier: 6.072A  pdb=" N   LYS g   3 " --> pdb=" O   GLN g  33 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   LYS g  35 " --> pdb=" O   LYS g   3 " (cutoff:3.500A)
      removed outlier: 5.740A  pdb=" N   LEU g   5 " --> pdb=" O   LYS g  35 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ALA g  37 " --> pdb=" O   LEU g   5 " (cutoff:3.500A)
      removed outlier: 5.818A  pdb=" N   PHE g   7 " --> pdb=" O   ALA g  37 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   VAL g  45 " --> pdb=" O   GLN g   4 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   THR g   6 " --> pdb=" O   VAL g  45 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   VAL g  47 " --> pdb=" O   THR g   6 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE g   8 " --> pdb=" O   VAL g  47 " (cutoff:3.500A)
      removed outlier: 6.277A  pdb=" N   ALA g  44 " --> pdb=" O   SER g 226 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   GLY g 228 " --> pdb=" O   ALA g  44 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   VAL g  46 " --> pdb=" O   GLY g 228 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   VAL g 216 " --> pdb=" O   ALA g  58 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   ALA g  58 " --> pdb=" O   VAL g 216 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   HIS g 218 " --> pdb=" O   HIS g  56 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   VAL g 190 " --> pdb=" O   ARG g 136 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1152 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: 2.35

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6094
        1.03 -     1.23: 4
        1.23 -     1.42: 2410
        1.42 -     1.61: 3643
        1.61 -     1.81: 18
  Bond restraints: 12169
  Sorted by residual:
  bond pdb=" CB  VAL h 152 "
       pdb=" CG1 VAL h 152 "
    ideal  model  delta    sigma   weight residual
    1.521  1.501  0.020 3.30e-02 9.18e+02 3.69e-01
  bond pdb=" CB  PRO g 185 "
       pdb=" CG  PRO g 185 "
    ideal  model  delta    sigma   weight residual
    1.492  1.521 -0.029 5.00e-02 4.00e+02 3.25e-01
  bond pdb=" CG  PRO d 296 "
       pdb=" CD  PRO d 296 "
    ideal  model  delta    sigma   weight residual
    1.503  1.486  0.017 3.40e-02 8.65e+02 2.62e-01
  bond pdb=" C   VAL g 172 "
       pdb=" O   VAL g 172 "
    ideal  model  delta    sigma   weight residual
    1.233  1.239 -0.006 1.25e-02 6.40e+03 2.49e-01
  bond pdb=" CB  ARG c  85 "
       pdb=" CG  ARG c  85 "
    ideal  model  delta    sigma   weight residual
    1.520  1.505  0.015 3.00e-02 1.11e+03 2.39e-01
  ... (remaining 12164 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 20324
        0.91 -     1.82: 1705
        1.82 -     2.74: 40
        2.74 -     3.65: 22
        3.65 -     4.56: 9
  Bond angle restraints: 22100
  Sorted by residual:
  angle pdb=" C   VAL g  79 "
        pdb=" N   ARG g  80 "
        pdb=" CA  ARG g  80 "
      ideal   model   delta    sigma   weight residual
     122.72  120.49    2.23 1.38e+00 5.25e-01 2.60e+00
  angle pdb=" C   THR g  57 "
        pdb=" N   ALA g  58 "
        pdb=" CA  ALA g  58 "
      ideal   model   delta    sigma   weight residual
     122.87  124.75   -1.88 1.44e+00 4.82e-01 1.70e+00
  angle pdb=" C   LEU g 193 "
        pdb=" N   ASN g 194 "
        pdb=" CA  ASN g 194 "
      ideal   model   delta    sigma   weight residual
     120.97  118.69    2.28 1.82e+00 3.02e-01 1.56e+00
  angle pdb=" C   HIS g  56 "
        pdb=" N   THR g  57 "
        pdb=" CA  THR g  57 "
      ideal   model   delta    sigma   weight residual
     122.62  120.79    1.83 1.56e+00 4.11e-01 1.38e+00
  angle pdb=" C   LEU d 295 "
        pdb=" N   PRO d 296 "
        pdb=" CD  PRO d 296 "
      ideal   model   delta    sigma   weight residual
     125.00  129.56   -4.56 4.10e+00 5.95e-02 1.24e+00
  ... (remaining 22095 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 5422
       17.81 -    35.61: 171
       35.61 -    53.42: 41
       53.42 -    71.23: 12
       71.23 -    89.03: 3
  Dihedral angle restraints: 5649
    sinusoidal: 3170
      harmonic: 2479
  Sorted by residual:
  dihedral pdb=" CA  GLU d 204 "
           pdb=" CB  GLU d 204 "
           pdb=" CG  GLU d 204 "
           pdb=" CD  GLU d 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.64   53.64     3      1.50e+01 4.44e-03 9.22e+00
  dihedral pdb=" N   ASP M 247 "
           pdb=" CA  ASP M 247 "
           pdb=" CB  ASP M 247 "
           pdb=" CG  ASP M 247 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  132.09   47.91     3      1.50e+01 4.44e-03 8.56e+00
  dihedral pdb=" CA  THR g  57 "
           pdb=" C   THR g  57 "
           pdb=" N   ALA g  58 "
           pdb=" CA  ALA g  58 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -165.54  -14.46     0      5.00e+00 4.00e-02 8.36e+00
  ... (remaining 5646 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 670
       0.029 -    0.058: 183
       0.058 -    0.086: 57
       0.086 -    0.115: 38
       0.115 -    0.144: 6
  Chirality restraints: 954
  Sorted by residual:
  chirality pdb=" CA  VAL d  58 "
            pdb=" N   VAL d  58 "
            pdb=" C   VAL d  58 "
            pdb=" CB  VAL d  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.19e-01
  chirality pdb=" CA  ILE g   8 "
            pdb=" N   ILE g   8 "
            pdb=" C   ILE g   8 "
            pdb=" CB  ILE g   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.95e-01
  chirality pdb=" CA  VAL g 196 "
            pdb=" N   VAL g 196 "
            pdb=" C   VAL g 196 "
            pdb=" CB  VAL g 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  ... (remaining 951 not shown)

  Planarity restraints: 1793
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA g  58 "   -0.019 2.00e-02 2.50e+03   3.77e-02 1.42e+01
        pdb=" C   ALA g  58 "    0.065 2.00e-02 2.50e+03
        pdb=" O   ALA g  58 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   VAL g  59 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP d 175 "    0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO d 176 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO d 176 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO d 176 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS d 237 "    0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO d 238 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO d 238 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO d 238 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1790 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 1024
        2.24 -     2.83: 28368
        2.83 -     3.42: 29681
        3.42 -     4.01: 39555
        4.01 -     4.60: 63427
  Nonbonded interactions: 162055
  Sorted by model distance:
  nonbonded pdb=" HE  ARG g  80 "
            pdb=" OE1 GLU g 203 "
     model   vdw
     1.654 2.450
  nonbonded pdb="HH22 ARG g  31 "
            pdb=" OE2 GLU g 250 "
     model   vdw
     1.684 2.450
  nonbonded pdb=" O   VAL g 196 "
            pdb=" HG1 THR g 199 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" OE2 GLU g  61 "
            pdb=" HZ2 LYS g 128 "
     model   vdw
     1.737 2.450
  nonbonded pdb=" HE1 TRP h 140 "
            pdb=" O   SER d  21 "
     model   vdw
     1.746 2.450
  ... (remaining 162050 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             16.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.080
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6071  Z= 0.105
  Angle     :  0.386   4.562   8207  Z= 0.202
  Chirality :  0.035   0.144    954
  Planarity :  0.003   0.038   1062
  Dihedral  :  8.105  89.035   2312
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 2.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.18 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.32), residues: 755
  helix:  3.01 (0.24), residues: 489
  sheet: -0.92 (0.61), residues: 62
  loop : -1.17 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG c  85 
 TYR   0.005   0.001   TYR h  87 
 PHE   0.006   0.001   PHE h  52 
 TRP   0.005   0.001   TRP d 112 
 HIS   0.003   0.001   HIS g  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 6071)
  covalent geometry    : angle       0.38593 ( 8207)
  hydrogen bonds       : bond        0.10358 (  387)
  hydrogen bonds       : angle       5.10583 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 161
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8287 (tt0) cc_final: 0.7949 (tt0)
REVERT: h   45 ASP cc_start: 0.8277 (t70) cc_final: 0.8011 (t0)
REVERT: h  146 LYS cc_start: 0.8520 (tttt) cc_final: 0.8250 (mtmm)
REVERT: c   86 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.7681 (ttm-80)
REVERT: c  113 ASN cc_start: 0.8286 (m110) cc_final: 0.8070 (m-40)
REVERT: d  170 VAL cc_start: 0.9214 (t) cc_final: 0.8991 (p)
  outliers start: 2
  outliers final: 2
  residues processed: 162
  average time/residue: 0.3233
  time to fit residues: 61.4755
Evaluate side-chains
  101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain g residue   60 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
d 125 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.119267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.102978 restraints weight = 32652.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107289 restraints weight = 14301.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.109982 restraints weight = 8179.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.111722 restraints weight = 5477.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.112908 restraints weight = 4042.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6071  Z= 0.140
  Angle     :  0.465   5.275   8207  Z= 0.244
  Chirality :  0.036   0.139    954
  Planarity :  0.004   0.033   1062
  Dihedral  :  3.893  47.726    836
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  5.45 %
    Favored  : 92.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.32), residues: 755
  helix:  2.89 (0.23), residues: 494
  sheet: -0.76 (0.63), residues: 62
  loop : -1.26 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG d  88 
 TYR   0.010   0.001   TYR M 214 
 PHE   0.012   0.001   PHE c  74 
 TRP   0.005   0.001   TRP d 175 
 HIS   0.003   0.001   HIS g  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6071)
  covalent geometry    : angle       0.46469 ( 8207)
  hydrogen bonds       : bond        0.03816 (  387)
  hydrogen bonds       : angle       4.31074 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ASN cc_start: 0.8344 (m110) cc_final: 0.8132 (m-40)
  outliers start: 10
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2115
  time to fit residues: 28.9240
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3417 r_free = 0.3417 target = 0.105643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.090318 restraints weight = 32811.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.094208 restraints weight = 15153.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.096714 restraints weight = 8877.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.098381 restraints weight = 6001.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.099531 restraints weight = 4445.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6071  Z= 0.183
  Angle     :  0.477   4.315   8207  Z= 0.253
  Chirality :  0.037   0.140    954
  Planarity :  0.004   0.034   1062
  Dihedral  :  3.987  47.683    836
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  7.63 %
    Favored  : 90.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.32), residues: 755
  helix:  2.67 (0.23), residues: 496
  sheet: -1.24 (0.63), residues: 65
  loop : -1.24 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG d  88 
 TYR   0.011   0.001   TYR M 214 
 PHE   0.012   0.001   PHE c  74 
 TRP   0.007   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6071)
  covalent geometry    : angle       0.47719 ( 8207)
  hydrogen bonds       : bond        0.03831 (  387)
  hydrogen bonds       : angle       4.30739 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ASN cc_start: 0.8329 (m110) cc_final: 0.8099 (m-40)
  outliers start: 10
  outliers final: 8
  residues processed: 99
  average time/residue: 0.2090
  time to fit residues: 26.2637
Evaluate side-chains
  100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  210 ASP
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.107670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.092404 restraints weight = 32012.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.096383 restraints weight = 14482.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.098908 restraints weight = 8419.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.100557 restraints weight = 5670.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101700 restraints weight = 4198.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.2821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6071  Z= 0.185
  Angle     :  0.481   4.246   8207  Z= 0.256
  Chirality :  0.037   0.138    954
  Planarity :  0.004   0.034   1062
  Dihedral  :  4.043  47.771    836
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  8.57 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.32), residues: 755
  helix:  2.60 (0.23), residues: 495
  sheet: -1.36 (0.63), residues: 65
  loop : -1.31 (0.44), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG d  88 
 TYR   0.008   0.001   TYR d 217 
 PHE   0.011   0.001   PHE c  74 
 TRP   0.008   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 6071)
  covalent geometry    : angle       0.48056 ( 8207)
  hydrogen bonds       : bond        0.03742 (  387)
  hydrogen bonds       : angle       4.28132 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: c  113 ASN cc_start: 0.8333 (m110) cc_final: 0.8095 (m-40)
  outliers start: 15
  outliers final: 12
  residues processed: 100
  average time/residue: 0.2020
  time to fit residues: 25.7102
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    6 THR
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue   70 LEU
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3443 r_free = 0.3443 target = 0.107245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.092062 restraints weight = 32171.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.096042 restraints weight = 14469.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.098573 restraints weight = 8364.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.100215 restraints weight = 5607.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.101295 restraints weight = 4135.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6071  Z= 0.174
  Angle     :  0.474   4.180   8207  Z= 0.251
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.035   1062
  Dihedral  :  4.044  47.639    836
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.19 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.32), residues: 755
  helix:  2.56 (0.24), residues: 495
  sheet: -1.50 (0.62), residues: 65
  loop : -1.28 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG d  88 
 TYR   0.009   0.001   TYR g 217 
 PHE   0.012   0.001   PHE c  74 
 TRP   0.007   0.001   TRP d 175 
 HIS   0.005   0.001   HIS g 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6071)
  covalent geometry    : angle       0.47372 ( 8207)
  hydrogen bonds       : bond        0.03702 (  387)
  hydrogen bonds       : angle       4.23546 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8357 (tt0) cc_final: 0.7755 (tt0)
REVERT: g  180 GLN cc_start: 0.8847 (tt0) cc_final: 0.8580 (tt0)
REVERT: c  113 ASN cc_start: 0.8351 (m110) cc_final: 0.8107 (m-40)
  outliers start: 14
  outliers final: 12
  residues processed: 96
  average time/residue: 0.1974
  time to fit residues: 24.2868
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  210 ASP
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3448 r_free = 0.3448 target = 0.107589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.092676 restraints weight = 31997.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.096609 restraints weight = 14370.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.099114 restraints weight = 8312.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.100769 restraints weight = 5543.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.101862 restraints weight = 4059.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6071  Z= 0.144
  Angle     :  0.465   4.116   8207  Z= 0.244
  Chirality :  0.036   0.140    954
  Planarity :  0.004   0.035   1062
  Dihedral  :  3.952  46.396    836
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.50 %
    Favored  : 88.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.32), residues: 755
  helix:  2.64 (0.24), residues: 495
  sheet: -1.55 (0.61), residues: 65
  loop : -1.21 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG d  88 
 TYR   0.008   0.001   TYR g 217 
 PHE   0.011   0.001   PHE c  74 
 TRP   0.006   0.001   TRP d 175 
 HIS   0.003   0.001   HIS c 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6071)
  covalent geometry    : angle       0.46465 ( 8207)
  hydrogen bonds       : bond        0.03518 (  387)
  hydrogen bonds       : angle       4.12311 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8376 (tt0) cc_final: 0.7713 (tt0)
REVERT: g   18 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: g  180 GLN cc_start: 0.8851 (tt0) cc_final: 0.8522 (tt0)
REVERT: c  113 ASN cc_start: 0.8336 (m110) cc_final: 0.8067 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 93
  average time/residue: 0.2004
  time to fit residues: 23.5538
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue   70 LEU
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    0.1980
   chunk 23 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.3457 r_free = 0.3457 target = 0.108174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.092995 restraints weight = 31818.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.097015 restraints weight = 14332.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.099547 restraints weight = 8283.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.101225 restraints weight = 5544.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.102367 restraints weight = 4068.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6071  Z= 0.122
  Angle     :  0.456   4.098   8207  Z= 0.238
  Chirality :  0.036   0.140    954
  Planarity :  0.004   0.035   1062
  Dihedral  :  3.864  45.278    836
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.50 %
    Favored  : 88.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.11 (0.32), residues: 755
  helix:  2.72 (0.24), residues: 496
  sheet: -1.50 (0.60), residues: 65
  loop : -1.17 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  86 
 TYR   0.008   0.001   TYR g 217 
 PHE   0.011   0.001   PHE c  74 
 TRP   0.005   0.001   TRP d 175 
 HIS   0.003   0.001   HIS c 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6071)
  covalent geometry    : angle       0.45607 ( 8207)
  hydrogen bonds       : bond        0.03366 (  387)
  hydrogen bonds       : angle       4.05009 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8361 (tt0) cc_final: 0.7729 (tt0)
REVERT: g   18 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: c  113 ASN cc_start: 0.8349 (m110) cc_final: 0.8072 (m-40)
  outliers start: 15
  outliers final: 14
  residues processed: 93
  average time/residue: 0.2165
  time to fit residues: 25.8712
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  210 ASP
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  103 MET
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.106732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.091500 restraints weight = 31890.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.095498 restraints weight = 14429.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.097997 restraints weight = 8344.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.099665 restraints weight = 5631.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.100768 restraints weight = 4162.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6071  Z= 0.183
  Angle     :  0.498   4.904   8207  Z= 0.263
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.036   1062
  Dihedral  :  3.917  44.630    836
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.81 %
    Favored  : 88.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.32), residues: 755
  helix:  2.60 (0.23), residues: 496
  sheet: -1.53 (0.61), residues: 65
  loop : -1.23 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG d 192 
 TYR   0.008   0.001   TYR d 217 
 PHE   0.010   0.001   PHE c  74 
 TRP   0.006   0.001   TRP d 175 
 HIS   0.005   0.001   HIS g 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6071)
  covalent geometry    : angle       0.49755 ( 8207)
  hydrogen bonds       : bond        0.03683 (  387)
  hydrogen bonds       : angle       4.18597 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8350 (tt0) cc_final: 0.7709 (tt0)
REVERT: c  113 ASN cc_start: 0.8386 (m110) cc_final: 0.8167 (m110)
  outliers start: 14
  outliers final: 14
  residues processed: 94
  average time/residue: 0.1850
  time to fit residues: 22.2707
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue   70 LEU
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  103 MET
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
g 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.107386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.092323 restraints weight = 31985.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.096343 restraints weight = 14367.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.098822 restraints weight = 8247.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.100465 restraints weight = 5553.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101575 restraints weight = 4083.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6071  Z= 0.140
  Angle     :  0.486   5.216   8207  Z= 0.256
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.037   1062
  Dihedral  :  3.869  43.815    836
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  9.81 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.32), residues: 755
  helix:  2.66 (0.23), residues: 496
  sheet: -1.56 (0.61), residues: 65
  loop : -1.15 (0.47), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG c  86 
 TYR   0.008   0.001   TYR g 217 
 PHE   0.010   0.001   PHE c  74 
 TRP   0.004   0.001   TRP d 175 
 HIS   0.003   0.001   HIS c 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6071)
  covalent geometry    : angle       0.48551 ( 8207)
  hydrogen bonds       : bond        0.03500 (  387)
  hydrogen bonds       : angle       4.09896 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8392 (tt0) cc_final: 0.7737 (tt0)
REVERT: c  113 ASN cc_start: 0.8387 (m110) cc_final: 0.8163 (m110)
  outliers start: 16
  outliers final: 14
  residues processed: 92
  average time/residue: 0.2000
  time to fit residues: 23.5928
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  210 ASP
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  103 MET
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
g 180 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.108524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.093518 restraints weight = 31940.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.097552 restraints weight = 14241.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100075 restraints weight = 8179.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.101705 restraints weight = 5448.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.102833 restraints weight = 4006.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6071  Z= 0.117
  Angle     :  0.486   5.381   8207  Z= 0.255
  Chirality :  0.036   0.140    954
  Planarity :  0.004   0.039   1062
  Dihedral  :  3.777  42.772    836
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 10.44 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.32), residues: 755
  helix:  2.79 (0.23), residues: 496
  sheet: -1.27 (0.62), residues: 62
  loop : -1.07 (0.47), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG c  86 
 TYR   0.007   0.001   TYR M 214 
 PHE   0.010   0.001   PHE c  74 
 TRP   0.004   0.001   TRP h  56 
 HIS   0.004   0.001   HIS c 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 6071)
  covalent geometry    : angle       0.48585 ( 8207)
  hydrogen bonds       : bond        0.03289 (  387)
  hydrogen bonds       : angle       3.98461 ( 1152)

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

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

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1510 Ramachandran restraints generated.
    755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: M  250 GLU cc_start: 0.8332 (tt0) cc_final: 0.7696 (tt0)
REVERT: c  113 ASN cc_start: 0.8367 (m110) cc_final: 0.8136 (m110)
  outliers start: 13
  outliers final: 13
  residues processed: 91
  average time/residue: 0.2052
  time to fit residues: 23.4397
Evaluate side-chains
  95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain M residue  212 VAL
Chi-restraints excluded: chain M residue  247 ASP
Chi-restraints excluded: chain h residue   39 ASN
Chi-restraints excluded: chain h residue   45 ASP
Chi-restraints excluded: chain h residue   59 GLU
Chi-restraints excluded: chain h residue  119 VAL
Chi-restraints excluded: chain g residue    5 LEU
Chi-restraints excluded: chain g residue   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain d residue  103 MET
Chi-restraints excluded: chain d residue  173 ILE
Chi-restraints excluded: chain d residue  245 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3438 r_free = 0.3438 target = 0.106841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.091895 restraints weight = 31945.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.095792 restraints weight = 14554.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.098285 restraints weight = 8480.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.099903 restraints weight = 5689.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.100958 restraints weight = 4204.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6071  Z= 0.185
  Angle     :  0.510   5.000   8207  Z= 0.272
  Chirality :  0.037   0.138    954
  Planarity :  0.004   0.036   1062
  Dihedral  :  3.834  42.775    836
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 10.44 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.05 (0.32), residues: 755
  helix:  2.67 (0.23), residues: 496
  sheet: -1.37 (0.64), residues: 62
  loop : -1.24 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG c  85 
 TYR   0.008   0.001   TYR g 217 
 PHE   0.009   0.001   PHE c  74 
 TRP   0.005   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 6071)
  covalent geometry    : angle       0.51049 ( 8207)
  hydrogen bonds       : bond        0.03625 (  387)
  hydrogen bonds       : angle       4.13219 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2384.64 seconds
wall clock time: 41 minutes 22.91 seconds (2482.91 seconds total)