Starting phenix.real_space_refine
on Wed Jul 30 01:55:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zw1_14991/07_2025/7zw1_14991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zw1_14991/07_2025/7zw1_14991.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/7zw1_14991/07_2025/7zw1_14991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zw1_14991/07_2025/7zw1_14991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zw1_14991/07_2025/7zw1_14991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zw1_14991/07_2025/7zw1_14991.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=   0.000 sd=   0.007
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      35      5.16       5
     C    3796      2.51       5
     N    1018      2.21       5
     O    1075      1.98       5
     H    5883      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 11807
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 5117
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 11, 'TRANS': 305}
    Chain: "B"
      Number of atoms: 4759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 316, 4759
          Classifications: {'peptide': 316}
          Link IDs: {'PTRANS': 19, 'TRANS': 296}
    Chain: "C"
      Number of atoms: 1931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1931
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
  Time building chain proxies: 7.85, per 1000 atoms: 0.66
  Number of scatterers: 11807
  At special positions: 0
  Unit cell: (69.536, 120.048, 139.072, 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      35     16.00
     O    1075      8.00
     N    1018      7.00
     C    3796      6.00
     H    5883      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 165 " - pdb=" SG  CYS A 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 166 " - pdb=" SG  CYS A 213 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 168 " - pdb=" SG  CYS B 253 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 169 " - pdb=" SG  CYS B 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 217 " - pdb=" SG  CYS B 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  98 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.40
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1378

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      61.4% alpha, 8.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 48
      removed outlier: 3.694A  pdb=" N   ARG A  48 " --> pdb=" O   GLU A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 87
      removed outlier: 3.920A  pdb=" N   ASP A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 93
      removed outlier: 4.398A  pdb=" N   ARG A  93 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 96
      No H-bonds generated for 'chain 'A' and resid 94 through 96'
    Processing helix  chain 'A' and resid 97 through 122
      removed outlier: 3.699A  pdb=" N   PHE A 120 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 140
      removed outlier: 4.326A  pdb=" N   LEU A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   GLU A 127 " --> pdb=" O   ARG A 123 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   ASN A 128 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   THR A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 164
      removed outlier: 4.271A  pdb=" N   LYS A 153 " --> pdb=" O   ARG A 149 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 177
    Processing helix  chain 'A' and resid 189 through 199
    Processing helix  chain 'A' and resid 210 through 214
    Processing helix  chain 'A' and resid 229 through 233
      removed outlier: 3.621A  pdb=" N   HIS A 233 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 293
    Processing helix  chain 'A' and resid 311 through 321
    Processing helix  chain 'B' and resid 10 through 48
      removed outlier: 4.121A  pdb=" N   HIS B  48 " --> pdb=" O   VAL B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 53
    Processing helix  chain 'B' and resid 60 through 89
      removed outlier: 3.727A  pdb=" N   GLN B  64 " --> pdb=" O   PRO B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 97
      Proline residue:  B  94  - end of helix
    Processing helix  chain 'B' and resid 99 through 143
      Proline residue:  B 126  - end of helix
      removed outlier: 3.747A  pdb=" N   LEU B 129 " --> pdb=" O   LEU B 125 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ASP B 130 " --> pdb=" O   PRO B 126 " (cutoff:3.500A)
      removed outlier: 4.990A  pdb=" N   GLU B 131 " --> pdb=" O   GLY B 127 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 167
      removed outlier: 4.431A  pdb=" N   ARG B 157 " --> pdb=" O   CYS B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 174 through 180
    Processing helix  chain 'B' and resid 184 through 188
    Processing helix  chain 'B' and resid 192 through 202
    Processing helix  chain 'B' and resid 203 through 206
      removed outlier: 3.776A  pdb=" N   LEU B 206 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 203 through 206'
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 252 through 297
      removed outlier: 3.876A  pdb=" N   GLY B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LEU B 296 " --> pdb=" O   ALA B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
    Processing helix  chain 'C' and resid 30 through 34
    Processing helix  chain 'C' and resid 64 through 67
    Processing helix  chain 'C' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 8
    Processing sheet with id=AA2, first strand: chain 'C' and resid 7 through 9
    Processing sheet with id=AA3, first strand: chain 'C' and resid 13 through 15
      removed outlier: 6.608A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA C  51 " --> pdb=" O   TRP C  38 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   CYS C  40 " --> pdb=" O   PHE C  49 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   PHE C  49 " --> pdb=" O   CYS C  40 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   TRP C  61 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 13 through 15
      removed outlier: 6.608A  pdb=" N   VAL C  14 " --> pdb=" O   SER C 127 " (cutoff:3.500A)

    378 hydrogen bonds defined for protein.
    1041 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: 4.47

  Time building geometry restraints manager: 4.62 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: 5874
        1.03 -     1.23: 9
        1.23 -     1.42: 2584
        1.42 -     1.62: 3436
        1.62 -     1.81: 47
  Bond restraints: 11950
  Sorted by residual:
  bond pdb=" CA  GLN B 246 "
       pdb=" CB  GLN B 246 "
    ideal  model  delta    sigma   weight residual
    1.526  1.537 -0.011 1.44e-02 4.82e+03 6.01e-01
  bond pdb=" CA  ASN B 247 "
       pdb=" CB  ASN B 247 "
    ideal  model  delta    sigma   weight residual
    1.530  1.542 -0.012 1.69e-02 3.50e+03 4.99e-01
  bond pdb=" N   LEU B   9 "
       pdb=" CA  LEU B   9 "
    ideal  model  delta    sigma   weight residual
    1.463  1.454  0.008 1.22e-02 6.72e+03 4.83e-01
  bond pdb=" CA  TYR B 174 "
       pdb=" CB  TYR B 174 "
    ideal  model  delta    sigma   weight residual
    1.536  1.526  0.010 1.46e-02 4.69e+03 4.79e-01
  bond pdb=" CA  GLY B 170 "
       pdb=" C   GLY B 170 "
    ideal  model  delta    sigma   weight residual
    1.514  1.524 -0.009 1.41e-02 5.03e+03 4.27e-01
  ... (remaining 11945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.81: 21420
        1.81 -     3.62: 135
        3.62 -     5.42: 17
        5.42 -     7.23: 1
        7.23 -     9.04: 1
  Bond angle restraints: 21574
  Sorted by residual:
  angle pdb=" CB  MET C  85 "
        pdb=" CG  MET C  85 "
        pdb=" SD  MET C  85 "
      ideal   model   delta    sigma   weight residual
     112.70  121.74   -9.04 3.00e+00 1.11e-01 9.08e+00
  angle pdb=" CA  TYR C 106 "
        pdb=" CB  TYR C 106 "
        pdb=" CG  TYR C 106 "
      ideal   model   delta    sigma   weight residual
     113.90  118.76   -4.86 1.80e+00 3.09e-01 7.30e+00
  angle pdb=" CA  VAL B 212 "
        pdb=" C   VAL B 212 "
        pdb=" N   PRO B 213 "
      ideal   model   delta    sigma   weight residual
     117.00  119.10   -2.10 9.50e-01 1.11e+00 4.88e+00
  angle pdb=" CA  MET C  85 "
        pdb=" CB  MET C  85 "
        pdb=" CG  MET C  85 "
      ideal   model   delta    sigma   weight residual
     114.10  118.39   -4.29 2.00e+00 2.50e-01 4.59e+00
  angle pdb=" CB  MET A 265 "
        pdb=" CG  MET A 265 "
        pdb=" SD  MET A 265 "
      ideal   model   delta    sigma   weight residual
     112.70  118.60   -5.90 3.00e+00 1.11e-01 3.87e+00
  ... (remaining 21569 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4910
       18.00 -    36.00: 456
       36.00 -    53.99: 220
       53.99 -    71.99: 43
       71.99 -    89.99: 7
  Dihedral angle restraints: 5636
    sinusoidal: 3043
      harmonic: 2593
  Sorted by residual:
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 222 "
           pdb=" CB  CYS A 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.92   48.08     1      1.00e+01 1.00e-02 3.19e+01
  dihedral pdb=" CB  CYS B 169 "
           pdb=" SG  CYS B 169 "
           pdb=" SG  CYS B 216 "
           pdb=" CB  CYS B 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  138.31  -45.31     1      1.00e+01 1.00e-02 2.85e+01
  dihedral pdb=" CB  CYS C  24 "
           pdb=" SG  CYS C  24 "
           pdb=" SG  CYS C  98 "
           pdb=" CB  CYS C  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.80   41.20     1      1.00e+01 1.00e-02 2.38e+01
  ... (remaining 5633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 694
       0.033 -    0.065: 136
       0.065 -    0.098: 57
       0.098 -    0.130: 17
       0.130 -    0.163: 3
  Chirality restraints: 907
  Sorted by residual:
  chirality pdb=" CA  MET C  85 "
            pdb=" N   MET C  85 "
            pdb=" C   MET C  85 "
            pdb=" CB  MET C  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.63e-01
  chirality pdb=" CA  VAL B 149 "
            pdb=" N   VAL B 149 "
            pdb=" C   VAL B 149 "
            pdb=" CB  VAL B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CA  VAL C  53 "
            pdb=" N   VAL C  53 "
            pdb=" C   VAL C  53 "
            pdb=" CB  VAL C  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.30e-01
  ... (remaining 904 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 106 "    0.018 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        pdb=" CG  TYR C 106 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 106 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 106 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 106 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 106 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 106 "   -0.001 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 106 "    0.001 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 106 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  62 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.45e+00
        pdb=" N   PRO B  63 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B  63 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B  63 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS B 253 "    0.005 2.00e-02 2.50e+03   1.04e-02 1.09e+00
        pdb=" C   CYS B 253 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   CYS B 253 "    0.007 2.00e-02 2.50e+03
        pdb=" N   HIS B 254 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 1330
        2.23 -     2.82: 25687
        2.82 -     3.41: 32081
        3.41 -     4.01: 40716
        4.01 -     4.60: 62067
  Nonbonded interactions: 161881
  Sorted by model distance:
  nonbonded pdb="HH21 ARG B 171 "
            pdb=" O   TYR C 106 "
     model   vdw
     1.634 2.450
  nonbonded pdb=" OD1 ASP A   9 "
            pdb=" H   LYS A  12 "
     model   vdw
     1.643 2.450
  nonbonded pdb=" OD1 ASP A 237 "
            pdb=" H   THR A 240 "
     model   vdw
     1.655 2.450
  nonbonded pdb="HD22 ASN B 202 "
            pdb=" O   LEU B 206 "
     model   vdw
     1.659 2.450
  nonbonded pdb=" O   VAL B  81 "
            pdb=" HG  SER B  84 "
     model   vdw
     1.661 2.450
  ... (remaining 161876 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:                  0.010
  Normalize map: mean=0, sd=1:             7.630
  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:             0.190
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.640
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
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   0.030   6074  Z= 0.109
  Angle     :  0.497   9.040   8253  Z= 0.259
  Chirality :  0.035   0.163    907
  Planarity :  0.003   0.039   1050
  Dihedral  : 17.278  89.990   2182
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 22.87 %
    Favored  : 76.97 %
  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:  3.09 (0.32), residues: 754
  helix:  3.84 (0.25), residues: 378
  sheet:  0.70 (0.67), residues: 58
  loop :  0.06 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  61 
 HIS   0.004   0.001   HIS C  54 
 PHE   0.009   0.001   PHE B 239 
 TYR   0.029   0.001   TYR C 106 
 ARG   0.003   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06890 (  374)
  hydrogen bonds       : angle       3.68718 ( 1041)
  SS BOND              : bond        0.00189 (    7)
  SS BOND              : angle       0.63152 (   14)
  covalent geometry    : bond        0.00220 ( 6067)
  covalent geometry    : angle       0.49713 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 31
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 32
  average time/residue: 0.5701
  time to fit residues: 25.3972
Evaluate side-chains
  30 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 62 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 31 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   chunk 37 optimal weight:    8.9990
   chunk 29 optimal weight:   30.0000
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   overall best weight:    2.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.066046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.054542 restraints weight = 123244.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.056390 restraints weight = 51974.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.057566 restraints weight = 29963.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.0437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6074  Z= 0.155
  Angle     :  0.501   4.976   8253  Z= 0.261
  Chirality :  0.035   0.135    907
  Planarity :  0.004   0.047   1050
  Dihedral  :  3.712  19.931    828
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 22.87 %
    Favored  : 76.50 %
  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:  2.89 (0.31), residues: 754
  helix:  3.69 (0.25), residues: 380
  sheet:  0.72 (0.67), residues: 58
  loop : -0.13 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  61 
 HIS   0.004   0.001   HIS B 172 
 PHE   0.014   0.001   PHE B 239 
 TYR   0.030   0.001   TYR C 106 
 ARG   0.011   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  374)
  hydrogen bonds       : angle       3.62338 ( 1041)
  SS BOND              : bond        0.00288 (    7)
  SS BOND              : angle       0.70298 (   14)
  covalent geometry    : bond        0.00328 ( 6067)
  covalent geometry    : angle       0.50078 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.904 
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: B  135 GLU cc_start: 0.8873 (tp30) cc_final: 0.8456 (tp30)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 0.5160
  time to fit residues: 24.7667
Evaluate side-chains
  34 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 53 optimal weight:    0.3980
   chunk 8 optimal weight:    9.9990
   chunk 21 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 56 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 263 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.063057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.051203 restraints weight = 110296.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.053165 restraints weight = 46544.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.054267 restraints weight = 26127.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.105
  Angle     :  0.472   5.450   8253  Z= 0.242
  Chirality :  0.035   0.134    907
  Planarity :  0.004   0.051   1050
  Dihedral  :  3.655  20.137    828
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 21.92 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.98 (0.31), residues: 754
  helix:  3.75 (0.25), residues: 380
  sheet:  0.76 (0.67), residues: 58
  loop : -0.06 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  61 
 HIS   0.003   0.001   HIS C  54 
 PHE   0.010   0.001   PHE B 239 
 TYR   0.032   0.001   TYR C 106 
 ARG   0.008   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (  374)
  hydrogen bonds       : angle       3.50931 ( 1041)
  SS BOND              : bond        0.00216 (    7)
  SS BOND              : angle       0.57979 (   14)
  covalent geometry    : bond        0.00225 ( 6067)
  covalent geometry    : angle       0.47206 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 1.158 
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: B  135 GLU cc_start: 0.8869 (tp30) cc_final: 0.8421 (tp30)
  outliers start: 8
  outliers final: 4
  residues processed: 40
  average time/residue: 0.4267
  time to fit residues: 24.0024
Evaluate side-chains
  35 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 73 optimal weight:    0.0170
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.7624

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.062172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.050580 restraints weight = 104679.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.052519 restraints weight = 42863.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.053719 restraints weight = 23581.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.0728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6074  Z= 0.138
  Angle     :  0.487   5.233   8253  Z= 0.253
  Chirality :  0.035   0.134    907
  Planarity :  0.004   0.055   1050
  Dihedral  :  3.694  20.544    828
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 22.87 %
    Favored  : 76.03 %
  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:  2.90 (0.31), residues: 754
  helix:  3.71 (0.25), residues: 380
  sheet:  0.70 (0.67), residues: 58
  loop : -0.15 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 236 
 PHE   0.014   0.001   PHE B 239 
 TYR   0.032   0.001   TYR C 106 
 ARG   0.008   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03479 (  374)
  hydrogen bonds       : angle       3.56035 ( 1041)
  SS BOND              : bond        0.00305 (    7)
  SS BOND              : angle       0.64987 (   14)
  covalent geometry    : bond        0.00294 ( 6067)
  covalent geometry    : angle       0.48640 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 7
  outliers final: 5
  residues processed: 38
  average time/residue: 0.3724
  time to fit residues: 19.5134
Evaluate side-chains
  36 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  288 TYR
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.9788

-------------------------------------------------------------------------------
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 = 0.3645 r_free = 0.3645 target = 0.061507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.049683 restraints weight = 110557.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.051540 restraints weight = 47203.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.052673 restraints weight = 26843.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6074  Z= 0.211
  Angle     :  0.534   5.649   8253  Z= 0.282
  Chirality :  0.036   0.132    907
  Planarity :  0.004   0.059   1050
  Dihedral  :  3.881  19.928    828
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 23.03 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.64 (0.31), residues: 754
  helix:  3.50 (0.25), residues: 380
  sheet:  0.58 (0.67), residues: 58
  loop : -0.26 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  61 
 HIS   0.004   0.001   HIS A  58 
 PHE   0.016   0.002   PHE B 239 
 TYR   0.037   0.002   TYR C 106 
 ARG   0.006   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  374)
  hydrogen bonds       : angle       3.72615 ( 1041)
  SS BOND              : bond        0.00452 (    7)
  SS BOND              : angle       0.78136 (   14)
  covalent geometry    : bond        0.00439 ( 6067)
  covalent geometry    : angle       0.53334 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  135 GLU cc_start: 0.8945 (tp30) cc_final: 0.8668 (tp30)
  outliers start: 15
  outliers final: 11
  residues processed: 47
  average time/residue: 0.3375
  time to fit residues: 22.1048
Evaluate side-chains
  45 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  278 THR
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   87 SER
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  234 TYR
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 63 optimal weight:   10.0000
   chunk 61 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3663 r_free = 0.3663 target = 0.062064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.050237 restraints weight = 110662.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.052122 restraints weight = 46735.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.053290 restraints weight = 26442.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6074  Z= 0.125
  Angle     :  0.490   5.616   8253  Z= 0.254
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.811  20.166    828
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 23.50 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.80 (0.31), residues: 754
  helix:  3.61 (0.25), residues: 380
  sheet:  0.61 (0.67), residues: 58
  loop : -0.14 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 
 PHE   0.011   0.001   PHE B 239 
 TYR   0.036   0.001   TYR C 106 
 ARG   0.007   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  374)
  hydrogen bonds       : angle       3.60749 ( 1041)
  SS BOND              : bond        0.00266 (    7)
  SS BOND              : angle       0.58864 (   14)
  covalent geometry    : bond        0.00266 ( 6067)
  covalent geometry    : angle       0.49027 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 1.030 
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: B  135 GLU cc_start: 0.8911 (tp30) cc_final: 0.8626 (tp30)
REVERT: C  110 MET cc_start: 0.5865 (mmt) cc_final: 0.5467 (mmm)
  outliers start: 10
  outliers final: 9
  residues processed: 41
  average time/residue: 0.3602
  time to fit residues: 21.5348
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  234 TYR
Chi-restraints excluded: chain C residue  106 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 63 optimal weight:    9.9990
   chunk 49 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 61 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
C  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.061324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.049469 restraints weight = 111879.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.051329 restraints weight = 47357.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.052464 restraints weight = 26897.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6074  Z= 0.204
  Angle     :  0.526   5.542   8253  Z= 0.278
  Chirality :  0.036   0.131    907
  Planarity :  0.004   0.059   1050
  Dihedral  :  3.915  20.218    828
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 23.50 %
    Favored  : 74.45 %
  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:  2.60 (0.31), residues: 754
  helix:  3.46 (0.25), residues: 379
  sheet:  0.51 (0.68), residues: 58
  loop : -0.26 (0.35), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  61 
 HIS   0.004   0.001   HIS B 236 
 PHE   0.015   0.001   PHE B 239 
 TYR   0.037   0.001   TYR C 106 
 ARG   0.007   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03670 (  374)
  hydrogen bonds       : angle       3.76699 ( 1041)
  SS BOND              : bond        0.00417 (    7)
  SS BOND              : angle       0.72323 (   14)
  covalent geometry    : bond        0.00427 ( 6067)
  covalent geometry    : angle       0.52575 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.898 
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: A  118 CYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8748 (p)
REVERT: B  135 GLU cc_start: 0.8947 (tp30) cc_final: 0.8651 (tp30)
REVERT: C  110 MET cc_start: 0.5888 (mmt) cc_final: 0.5502 (mmm)
  outliers start: 13
  outliers final: 11
  residues processed: 44
  average time/residue: 0.3409
  time to fit residues: 21.2104
Evaluate side-chains
  42 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 30
  time to evaluate  : 0.896 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  234 TYR
Chi-restraints excluded: chain B residue  288 TYR
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
C  41 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.062085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.050300 restraints weight = 110996.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.052184 restraints weight = 46744.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.053351 restraints weight = 26498.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.114
  Angle     :  0.485   5.563   8253  Z= 0.251
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.058   1050
  Dihedral  :  3.816  20.560    828
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 23.97 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.84 (0.32), residues: 754
  helix:  3.65 (0.25), residues: 379
  sheet:  0.57 (0.67), residues: 58
  loop : -0.11 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 
 PHE   0.010   0.001   PHE B 239 
 TYR   0.036   0.001   TYR C 106 
 ARG   0.007   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  374)
  hydrogen bonds       : angle       3.58258 ( 1041)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       0.53707 (   14)
  covalent geometry    : bond        0.00245 ( 6067)
  covalent geometry    : angle       0.48510 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.874 
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: A  118 CYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8754 (p)
REVERT: B  135 GLU cc_start: 0.8911 (tp30) cc_final: 0.8603 (tp30)
REVERT: C  110 MET cc_start: 0.5906 (mmt) cc_final: 0.5565 (mmt)
  outliers start: 14
  outliers final: 12
  residues processed: 45
  average time/residue: 0.3205
  time to fit residues: 20.4742
Evaluate side-chains
  45 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 HIS
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  234 TYR
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 8 optimal weight:    0.3980
   chunk 45 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   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 = 0.3690 r_free = 0.3690 target = 0.062908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.051186 restraints weight = 109643.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.053113 restraints weight = 46206.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.054295 restraints weight = 25961.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6074  Z= 0.095
  Angle     :  0.477   7.234   8253  Z= 0.243
  Chirality :  0.035   0.139    907
  Planarity :  0.004   0.058   1050
  Dihedral  :  3.670  21.821    828
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 24.29 %
    Favored  : 73.97 %
  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:  3.03 (0.32), residues: 754
  helix:  3.80 (0.25), residues: 380
  sheet:  0.55 (0.66), residues: 58
  loop :  0.00 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  61 
 HIS   0.002   0.001   HIS B 236 
 PHE   0.008   0.001   PHE B 239 
 TYR   0.034   0.001   TYR C 106 
 ARG   0.008   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  374)
  hydrogen bonds       : angle       3.48622 ( 1041)
  SS BOND              : bond        0.00170 (    7)
  SS BOND              : angle       0.45949 (   14)
  covalent geometry    : bond        0.00206 ( 6067)
  covalent geometry    : angle       0.47733 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.951 
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: A  118 CYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8768 (p)
REVERT: B  135 GLU cc_start: 0.8872 (tp30) cc_final: 0.8559 (tp30)
REVERT: C  110 MET cc_start: 0.5862 (mmt) cc_final: 0.5586 (mmt)
  outliers start: 11
  outliers final: 8
  residues processed: 42
  average time/residue: 0.3629
  time to fit residues: 21.6191
Evaluate side-chains
  40 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 46 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 54 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.062470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.050724 restraints weight = 110352.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.052639 restraints weight = 46569.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.053782 restraints weight = 26202.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6074  Z= 0.112
  Angle     :  0.480   6.555   8253  Z= 0.246
  Chirality :  0.035   0.135    907
  Planarity :  0.004   0.057   1050
  Dihedral  :  3.654  22.309    828
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 24.61 %
    Favored  : 73.66 %
  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:  3.01 (0.32), residues: 754
  helix:  3.80 (0.25), residues: 380
  sheet:  0.54 (0.66), residues: 58
  loop : -0.03 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 236 
 PHE   0.011   0.001   PHE B 239 
 TYR   0.034   0.001   TYR C 106 
 ARG   0.006   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  374)
  hydrogen bonds       : angle       3.51436 ( 1041)
  SS BOND              : bond        0.00226 (    7)
  SS BOND              : angle       0.51439 (   14)
  covalent geometry    : bond        0.00242 ( 6067)
  covalent geometry    : angle       0.48017 ( 8239)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 1.545 
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: A   23 MET cc_start: 0.7795 (ttp) cc_final: 0.7549 (mtt)
REVERT: A  118 CYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8774 (p)
REVERT: B  135 GLU cc_start: 0.8902 (tp30) cc_final: 0.8581 (tp30)
REVERT: C  110 MET cc_start: 0.5891 (mmt) cc_final: 0.5572 (mmm)
  outliers start: 11
  outliers final: 9
  residues processed: 42
  average time/residue: 0.4903
  time to fit residues: 29.6987
Evaluate side-chains
  42 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 CYS
Chi-restraints excluded: chain A residue  241 GLU
Chi-restraints excluded: chain A residue  250 CYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain B residue   23 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  288 TYR
Chi-restraints excluded: chain C residue  106 TYR
Chi-restraints excluded: chain C residue  116 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    0.4980
   chunk 67 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    2.0988

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.061928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.050171 restraints weight = 110151.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.052053 restraints weight = 46932.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.053200 restraints weight = 26529.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6074  Z= 0.155
  Angle     :  0.500   6.378   8253  Z= 0.260
  Chirality :  0.035   0.133    907
  Planarity :  0.004   0.058   1050
  Dihedral  :  3.711  22.164    828
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 24.61 %
    Favored  : 73.50 %
  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:  2.88 (0.32), residues: 754
  helix:  3.70 (0.25), residues: 379
  sheet:  0.57 (0.67), residues: 58
  loop : -0.12 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  61 
 HIS   0.003   0.001   HIS B 236 
 PHE   0.021   0.001   PHE A 275 
 TYR   0.035   0.001   TYR C 106 
 ARG   0.006   0.000   ARG B 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03472 (  374)
  hydrogen bonds       : angle       3.60247 ( 1041)
  SS BOND              : bond        0.00320 (    7)
  SS BOND              : angle       0.60938 (   14)
  covalent geometry    : bond        0.00328 ( 6067)
  covalent geometry    : angle       0.50019 ( 8239)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4431.89 seconds
wall clock time: 79 minutes 30.35 seconds (4770.35 seconds total)