Starting phenix.real_space_refine
on Wed Jul 30 05:17:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ap8_15561/07_2025/8ap8_15561.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ap8_15561/07_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_15561/07_2025/8ap8_15561.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ap8_15561/07_2025/8ap8_15561.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ap8_15561/07_2025/8ap8_15561.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ap8_15561/07_2025/8ap8_15561.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.44, per 1000 atoms: 0.70
  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: 3.23
  Conformation dependent library (CDL) restraints added in 982.7 milliseconds
  

  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: 0.88
  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: 4.13

  Time building geometry restraints manager: 3.94 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:             8.390
  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:             0.200
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     30.810
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.140
-------------------------------------------------------------------------------
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 : 2.40
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (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
 TRP   0.005   0.001   TRP d 112 
 HIS   0.003   0.001   HIS g  56 
 PHE   0.006   0.001   PHE h  52 
 TYR   0.005   0.001   TYR h  87 
 ARG   0.001   0.000   ARG c  85 

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

*********************** 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  : 0.892 
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: 0.6445
  time to fit residues: 123.3413
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  : 1.065 
-------------------------------------------------------------------------------
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 62 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    0.3980
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3623 r_free = 0.3623 target = 0.118548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.102326 restraints weight = 32453.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.106593 restraints weight = 14304.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.109300 restraints weight = 8202.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2104

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= 0.153
  Angle     :  0.470   5.216   8207  Z= 0.248
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.034   1062
  Dihedral  :  3.930  47.743    836
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  5.76 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.32), residues: 755
  helix:  2.83 (0.23), residues: 495
  sheet: -0.72 (0.64), residues: 61
  loop : -1.29 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d 175 
 HIS   0.003   0.001   HIS g  56 
 PHE   0.013   0.001   PHE c  74 
 TYR   0.011   0.001   TYR M 214 
 ARG   0.003   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  387)
  hydrogen bonds       : angle       4.35343 ( 1152)
  covalent geometry    : bond        0.00344 ( 6071)
  covalent geometry    : angle       0.46998 ( 8207)

*********************** 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
  114 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.911 
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: c  113 ASN cc_start: 0.8348 (m110) cc_final: 0.8140 (m-40)
  outliers start: 10
  outliers final: 6
  residues processed: 109
  average time/residue: 0.5043
  time to fit residues: 68.6254
Evaluate side-chains
  100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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 30 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0370
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.7860

-------------------------------------------------------------------------------
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 = 0.3424 r_free = 0.3424 target = 0.106204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.090915 restraints weight = 32597.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.094812 restraints weight = 15035.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.097335 restraints weight = 8807.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2551

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= 0.164
  Angle     :  0.467   4.280   8207  Z= 0.246
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.034   1062
  Dihedral  :  3.971  48.021    836
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  :  7.79 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.32), residues: 755
  helix:  2.71 (0.23), residues: 496
  sheet: -1.29 (0.62), residues: 65
  loop : -1.25 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP d 175 
 HIS   0.004   0.001   HIS c 103 
 PHE   0.012   0.001   PHE c  74 
 TYR   0.013   0.001   TYR M 214 
 ARG   0.004   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03738 (  387)
  hydrogen bonds       : angle       4.27438 ( 1152)
  covalent geometry    : bond        0.00370 ( 6071)
  covalent geometry    : angle       0.46666 ( 8207)

*********************** 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
  107 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.986 
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: g   98 ASP cc_start: 0.8672 (t0) cc_final: 0.8469 (t0)
REVERT: c  113 ASN cc_start: 0.8334 (m110) cc_final: 0.8104 (m-40)
  outliers start: 12
  outliers final: 10
  residues processed: 100
  average time/residue: 0.4845
  time to fit residues: 61.1518
Evaluate side-chains
  103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
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  119 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    0.2980
   chunk 66 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3402 r_free = 0.3402 target = 0.104651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.089557 restraints weight = 32586.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093406 restraints weight = 15067.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.095876 restraints weight = 8849.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.2816

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     :  0.470   4.230   8207  Z= 0.250
  Chirality :  0.037   0.138    954
  Planarity :  0.004   0.038   1062
  Dihedral  :  4.014  47.851    836
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  8.26 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.32), residues: 755
  helix:  2.64 (0.23), residues: 495
  sheet: -1.37 (0.62), residues: 65
  loop : -1.29 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP d 175 
 HIS   0.005   0.001   HIS g 229 
 PHE   0.011   0.001   PHE d 236 
 TYR   0.009   0.001   TYR d 217 
 ARG   0.005   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  387)
  hydrogen bonds       : angle       4.24664 ( 1152)
  covalent geometry    : bond        0.00394 ( 6071)
  covalent geometry    : angle       0.46969 ( 8207)

*********************** 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
  104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.905 
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: g   98 ASP cc_start: 0.8701 (t0) cc_final: 0.8436 (t0)
REVERT: g  180 GLN cc_start: 0.8835 (tt0) cc_final: 0.8564 (tt0)
REVERT: c  113 ASN cc_start: 0.8361 (m110) cc_final: 0.8125 (m-40)
  outliers start: 13
  outliers final: 11
  residues processed: 99
  average time/residue: 0.4614
  time to fit residues: 57.6971
Evaluate side-chains
  100 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
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   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 49 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.104724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.089574 restraints weight = 32353.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093430 restraints weight = 15018.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.095920 restraints weight = 8827.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6071  Z= 0.155
  Angle     :  0.469   4.172   8207  Z= 0.247
  Chirality :  0.036   0.139    954
  Planarity :  0.004   0.039   1062
  Dihedral  :  3.989  47.095    836
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.35 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.32), residues: 755
  helix:  2.67 (0.24), residues: 495
  sheet: -1.45 (0.61), residues: 65
  loop : -1.28 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 
 PHE   0.011   0.001   PHE c  74 
 TYR   0.008   0.001   TYR g 217 
 ARG   0.006   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03600 (  387)
  hydrogen bonds       : angle       4.18632 ( 1152)
  covalent geometry    : bond        0.00355 ( 6071)
  covalent geometry    : angle       0.46862 ( 8207)

*********************** 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
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.918 
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: g   18 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7712 (tm-30)
REVERT: g   98 ASP cc_start: 0.8694 (t0) cc_final: 0.8422 (t0)
REVERT: c  113 ASN cc_start: 0.8353 (m110) cc_final: 0.8109 (m-40)
  outliers start: 11
  outliers final: 10
  residues processed: 95
  average time/residue: 0.4660
  time to fit residues: 55.5901
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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   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 69 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 58 optimal weight:    0.3980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3396 r_free = 0.3396 target = 0.104236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.089113 restraints weight = 32983.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.092975 restraints weight = 15187.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095450 restraints weight = 8895.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6071  Z= 0.167
  Angle     :  0.476   4.444   8207  Z= 0.251
  Chirality :  0.036   0.139    954
  Planarity :  0.004   0.043   1062
  Dihedral  :  3.968  46.125    836
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  :  9.35 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.32), residues: 755
  helix:  2.65 (0.24), residues: 495
  sheet: -1.47 (0.61), residues: 65
  loop : -1.30 (0.45), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 
 PHE   0.012   0.001   PHE c  74 
 TYR   0.009   0.001   TYR h  87 
 ARG   0.007   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  387)
  hydrogen bonds       : angle       4.17498 ( 1152)
  covalent geometry    : bond        0.00384 ( 6071)
  covalent geometry    : angle       0.47571 ( 8207)

*********************** 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
  99 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 1.010 
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: M  245 GLN cc_start: 0.8541 (tp40) cc_final: 0.8137 (tp40)
REVERT: g   98 ASP cc_start: 0.8686 (t0) cc_final: 0.8432 (t0)
REVERT: g  180 GLN cc_start: 0.8842 (tt0) cc_final: 0.8573 (tt0)
REVERT: c  113 ASN cc_start: 0.8348 (m110) cc_final: 0.8093 (m-40)
  outliers start: 14
  outliers final: 13
  residues processed: 93
  average time/residue: 0.4947
  time to fit residues: 58.0235
Evaluate side-chains
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
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   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 c residue  106 ASP
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 55 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0980
   chunk 53 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.104239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.089228 restraints weight = 32430.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.093112 restraints weight = 14926.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.095577 restraints weight = 8723.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.3136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6071  Z= 0.153
  Angle     :  0.470   4.396   8207  Z= 0.247
  Chirality :  0.036   0.139    954
  Planarity :  0.004   0.047   1062
  Dihedral  :  3.940  45.222    836
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  9.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.32), residues: 755
  helix:  2.70 (0.24), residues: 496
  sheet: -1.50 (0.61), residues: 65
  loop : -1.28 (0.45), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 
 PHE   0.012   0.001   PHE c  74 
 TYR   0.008   0.001   TYR d 217 
 ARG   0.007   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03529 (  387)
  hydrogen bonds       : angle       4.13517 ( 1152)
  covalent geometry    : bond        0.00351 ( 6071)
  covalent geometry    : angle       0.47000 ( 8207)

*********************** 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: 17
    poor density    : 82
  time to evaluate  : 0.988 
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: g   18 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7727 (tm-30)
REVERT: g   98 ASP cc_start: 0.8664 (t0) cc_final: 0.8399 (t0)
REVERT: g  180 GLN cc_start: 0.8838 (tt0) cc_final: 0.8498 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 91
  average time/residue: 0.4716
  time to fit residues: 54.3144
Evaluate side-chains
  95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain c residue  106 ASP
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 44 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 52 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0030
   chunk 41 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5990

-------------------------------------------------------------------------------
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 = 0.3400 r_free = 0.3400 target = 0.104625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.089537 restraints weight = 32747.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.093470 restraints weight = 15045.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.095974 restraints weight = 8766.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3148

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= 0.137
  Angle     :  0.470   4.730   8207  Z= 0.247
  Chirality :  0.036   0.139    954
  Planarity :  0.004   0.050   1062
  Dihedral  :  3.872  44.397    836
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.66 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.32), residues: 755
  helix:  2.73 (0.24), residues: 496
  sheet: -1.56 (0.61), residues: 65
  loop : -1.19 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d 175 
 HIS   0.003   0.001   HIS c 103 
 PHE   0.011   0.001   PHE c  74 
 TYR   0.008   0.001   TYR h  87 
 ARG   0.008   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03435 (  387)
  hydrogen bonds       : angle       4.09156 ( 1152)
  covalent geometry    : bond        0.00315 ( 6071)
  covalent geometry    : angle       0.46984 ( 8207)

*********************** 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
  98 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.929 
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: g   18 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7710 (tm-30)
REVERT: g   98 ASP cc_start: 0.8661 (t0) cc_final: 0.8406 (t0)
REVERT: c   86 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8296 (ttm-80)
  outliers start: 15
  outliers final: 14
  residues processed: 91
  average time/residue: 0.4707
  time to fit residues: 54.0803
Evaluate side-chains
  94 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
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   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 c residue  106 ASP
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 62 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 52 optimal weight:    0.4980
   chunk 66 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.104041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.089096 restraints weight = 32835.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.092995 restraints weight = 15042.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095468 restraints weight = 8739.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8283
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6071  Z= 0.160
  Angle     :  0.495   5.074   8207  Z= 0.261
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.036   1062
  Dihedral  :  3.878  44.105    836
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.81 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.32), residues: 755
  helix:  2.70 (0.24), residues: 496
  sheet: -1.37 (0.63), residues: 62
  loop : -1.28 (0.45), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 
 PHE   0.011   0.001   PHE c  74 
 TYR   0.008   0.001   TYR g 217 
 ARG   0.007   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03519 (  387)
  hydrogen bonds       : angle       4.13968 ( 1152)
  covalent geometry    : bond        0.00367 ( 6071)
  covalent geometry    : angle       0.49502 ( 8207)

*********************** 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
  95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.917 
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: g   98 ASP cc_start: 0.8669 (t0) cc_final: 0.8413 (t0)
REVERT: c   86 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8240 (ttm-80)
  outliers start: 15
  outliers final: 13
  residues processed: 88
  average time/residue: 0.4609
  time to fit residues: 51.6675
Evaluate side-chains
  93 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
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   32 VAL
Chi-restraints excluded: chain g residue   60 THR
Chi-restraints excluded: chain g residue  179 ASN
Chi-restraints excluded: chain c residue  106 ASP
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 2 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 43 optimal weight:    0.4980
   chunk 66 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0270
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5238

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.104835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.089939 restraints weight = 32443.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.093856 restraints weight = 14858.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.096355 restraints weight = 8616.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6071  Z= 0.130
  Angle     :  0.484   5.547   8207  Z= 0.255
  Chirality :  0.037   0.140    954
  Planarity :  0.004   0.035   1062
  Dihedral  :  3.816  43.142    836
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  9.81 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.32), residues: 755
  helix:  2.75 (0.24), residues: 497
  sheet: -1.45 (0.62), residues: 62
  loop : -1.09 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP d 175 
 HIS   0.003   0.001   HIS c 103 
 PHE   0.011   0.001   PHE c  74 
 TYR   0.009   0.001   TYR M 214 
 ARG   0.007   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  387)
  hydrogen bonds       : angle       4.06521 ( 1152)
  covalent geometry    : bond        0.00299 ( 6071)
  covalent geometry    : angle       0.48446 ( 8207)

********************** 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
  96 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.895 
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: g   98 ASP cc_start: 0.8678 (t0) cc_final: 0.8406 (t0)
REVERT: c   86 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8244 (ttm-80)
  outliers start: 15
  outliers final: 14
  residues processed: 87
  average time/residue: 0.4546
  time to fit residues: 50.1874
Evaluate side-chains
  95 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
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   91 GLU
Chi-restraints excluded: chain h residue  119 VAL
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 c residue  106 ASP
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 49 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.103619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.088611 restraints weight = 32938.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.092515 restraints weight = 15172.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.094987 restraints weight = 8818.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6071  Z= 0.172
  Angle     :  0.503   5.213   8207  Z= 0.267
  Chirality :  0.037   0.139    954
  Planarity :  0.004   0.036   1062
  Dihedral  :  3.857  42.856    836
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  :  9.66 %
    Favored  : 87.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.32), residues: 755
  helix:  2.67 (0.23), residues: 496
  sheet: -1.62 (0.62), residues: 62
  loop : -1.23 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP d 175 
 HIS   0.004   0.001   HIS g 229 
 PHE   0.011   0.001   PHE c  74 
 TYR   0.008   0.001   TYR g 217 
 ARG   0.006   0.000   ARG d  88 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03611 (  387)
  hydrogen bonds       : angle       4.15400 ( 1152)
  covalent geometry    : bond        0.00395 ( 6071)
  covalent geometry    : angle       0.50311 ( 8207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5559.88 seconds
wall clock time: 98 minutes 9.40 seconds (5889.40 seconds total)