Starting phenix.real_space_refine
on Tue Feb 11 11:52:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fci_31526/02_2025/7fci_31526.cif"
  }
  resolution = 3.3
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    3622      2.51       5
     N     899      2.21       5
     O    1045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5613
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2280
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 16, 'TRANS': 280}
    Chain: "L"
      Number of atoms: 1640
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1640
          Classifications: {'peptide': 213}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 202}
    Chain: "H"
      Number of atoms: 1693
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1693
          Classifications: {'peptide': 224}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 208}
  Time building chain proxies: 3.93, per 1000 atoms: 0.70
  Number of scatterers: 5613
  At special positions: 0
  Unit cell: (57.201, 66.32, 135.127, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1045      8.00
     N     899      7.00
     C    3622      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 133 " - pdb=" SG  CYS L 193 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 149 " - pdb=" SG  CYS H 204 " 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: 1.45
  Conformation dependent library (CDL) restraints added in 760.9 milliseconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1362

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 11 sheets defined
      41.4% alpha, 27.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 43
      removed outlier: 3.900A  pdb=" N   ASP A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A  26 " --> pdb=" O   PRO A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.544A  pdb=" N   LYS A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 71
    Processing helix  chain 'A' and resid 71 through 83
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 103 through 112
    Processing helix  chain 'A' and resid 115 through 143
      removed outlier: 3.569A  pdb=" N   ILE A 120 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   VAL A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
      Proline residue:  A 135  - end of helix
    Processing helix  chain 'A' and resid 155 through 180
      Proline residue:  A 169  - end of helix
    Processing helix  chain 'A' and resid 180 through 216
      removed outlier: 3.824A  pdb=" N   MET A 184 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ARG A 185 " --> pdb=" O   PRO A 181 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   TYR A 186 " --> pdb=" O   GLN A 182 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU A 197 " --> pdb=" O   ILE A 193 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   MET A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 244
      Proline residue:  A 230  - end of helix
    Processing helix  chain 'A' and resid 247 through 260
      removed outlier: 3.689A  pdb=" N   ARG A 252 " --> pdb=" O   GLY A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 274
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 281 through 283
      No H-bonds generated for 'chain 'A' and resid 281 through 283'
    Processing helix  chain 'A' and resid 284 through 310
    Processing helix  chain 'L' and resid 78 through 82
      removed outlier: 3.566A  pdb=" N   ASP L  81 " --> pdb=" O   GLU L  78 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ALA L  82 " --> pdb=" O   ALA L  79 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 78 through 82'
    Processing helix  chain 'L' and resid 120 through 127
    Processing helix  chain 'L' and resid 182 through 188
      removed outlier: 3.775A  pdb=" N   HIS L 188 " --> pdb=" O   GLU L 184 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 4.057A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.529A  pdb=" N   ASP H  90 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   SER H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'H' and resid 165 through 167
      No H-bonds generated for 'chain 'H' and resid 165 through 167'
    Processing helix  chain 'H' and resid 195 through 200
    Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.778A  pdb=" N   GLN L  36 " --> pdb=" O   LEU L  45 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   LEU L  45 " --> pdb=" O   GLN L  36 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.620A  pdb=" N   THR L  96 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 115 through 117
      removed outlier: 3.852A  pdb=" N   VAL L 132 " --> pdb=" O   PHE L 117 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   TYR L 172 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 152 through 153
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA7, first strand: chain 'H' and resid 9 through 12
      removed outlier: 3.597A  pdb=" N   GLU H  10 " --> pdb=" O   SER H 117 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR H 119 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   MET H  34 " --> pdb=" O   GLU H  50 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLU H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 9 through 12
      removed outlier: 3.597A  pdb=" N   GLU H  10 " --> pdb=" O   SER H 117 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR H 119 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 133
      removed outlier: 3.703A  pdb=" N   GLY H 148 " --> pdb=" O   LEU H 133 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   CYS H 149 " --> pdb=" O   SER H 188 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   SER H 188 " --> pdb=" O   CYS H 149 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 160 through 163
    Processing sheet with id=AB2, first strand: chain 'H' and resid 178 through 180

    331 hydrogen bonds defined for protein.
    915 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: 1.71

  Time building geometry restraints manager: 1.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1549
        1.34 -     1.45: 1038
        1.45 -     1.57: 3090
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 5749
  Sorted by residual:
  bond pdb=" CB  PRO A 220 "
       pdb=" CG  PRO A 220 "
    ideal  model  delta    sigma   weight residual
    1.492  1.558 -0.066 5.00e-02 4.00e+02 1.73e+00
  bond pdb=" CB  GLU A 257 "
       pdb=" CG  GLU A 257 "
    ideal  model  delta    sigma   weight residual
    1.520  1.557 -0.037 3.00e-02 1.11e+03 1.50e+00
  bond pdb=" CG  PRO L  94 "
       pdb=" CD  PRO L  94 "
    ideal  model  delta    sigma   weight residual
    1.512  1.484  0.028 2.70e-02 1.37e+03 1.09e+00
  bond pdb=" CA  VAL H 159 "
       pdb=" CB  VAL H 159 "
    ideal  model  delta    sigma   weight residual
    1.551  1.540  0.011 1.08e-02 8.57e+03 9.47e-01
  bond pdb=" CA  VAL H 106 "
       pdb=" CB  VAL H 106 "
    ideal  model  delta    sigma   weight residual
    1.532  1.546 -0.014 1.47e-02 4.63e+03 9.15e-01
  ... (remaining 5744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 7696
        2.01 -     4.01: 102
        4.01 -     6.02: 15
        6.02 -     8.02: 3
        8.02 -    10.03: 1
  Bond angle restraints: 7817
  Sorted by residual:
  angle pdb=" CA  GLU A 257 "
        pdb=" CB  GLU A 257 "
        pdb=" CG  GLU A 257 "
      ideal   model   delta    sigma   weight residual
     114.10  120.71   -6.61 2.00e+00 2.50e-01 1.09e+01
  angle pdb=" CA  LEU A 165 "
        pdb=" CB  LEU A 165 "
        pdb=" CG  LEU A 165 "
      ideal   model   delta    sigma   weight residual
     116.30  126.33  -10.03 3.50e+00 8.16e-02 8.21e+00
  angle pdb=" CB  GLU A 257 "
        pdb=" CG  GLU A 257 "
        pdb=" CD  GLU A 257 "
      ideal   model   delta    sigma   weight residual
     112.60  116.99   -4.39 1.70e+00 3.46e-01 6.68e+00
  angle pdb=" CA  TYR L  31 "
        pdb=" CB  TYR L  31 "
        pdb=" CG  TYR L  31 "
      ideal   model   delta    sigma   weight residual
     113.90  118.30   -4.40 1.80e+00 3.09e-01 5.97e+00
  angle pdb=" CA  GLY H 115 "
        pdb=" C   GLY H 115 "
        pdb=" O   GLY H 115 "
      ideal   model   delta    sigma   weight residual
     122.22  120.63    1.59 6.50e-01 2.37e+00 5.95e+00
  ... (remaining 7812 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 2913
       16.35 -    32.69: 367
       32.69 -    49.04: 124
       49.04 -    65.38: 28
       65.38 -    81.73: 4
  Dihedral angle restraints: 3436
    sinusoidal: 1310
      harmonic: 2126
  Sorted by residual:
  dihedral pdb=" CB  CYS H 149 "
           pdb=" SG  CYS H 149 "
           pdb=" SG  CYS H 204 "
           pdb=" CB  CYS H 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.94  -67.94     1      1.00e+01 1.00e-02 5.99e+01
  dihedral pdb=" CA  ASN L  30 "
           pdb=" C   ASN L  30 "
           pdb=" N   TYR L  31 "
           pdb=" CA  TYR L  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.47   21.53     0      5.00e+00 4.00e-02 1.85e+01
  dihedral pdb=" CA  GLY A 132 "
           pdb=" C   GLY A 132 "
           pdb=" N   MET A 133 "
           pdb=" CA  MET A 133 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.30  -17.70     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 3433 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 533
       0.027 -    0.054: 241
       0.054 -    0.080: 70
       0.080 -    0.107: 44
       0.107 -    0.134: 20
  Chirality restraints: 908
  Sorted by residual:
  chirality pdb=" CA  VAL H 206 "
            pdb=" N   VAL H 206 "
            pdb=" C   VAL H 206 "
            pdb=" CB  VAL H 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  VAL H 161 "
            pdb=" N   VAL H 161 "
            pdb=" C   VAL H 161 "
            pdb=" CB  VAL H 161 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  PRO A 220 "
            pdb=" N   PRO A 220 "
            pdb=" C   PRO A 220 "
            pdb=" CB  PRO A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.39e-01
  ... (remaining 905 not shown)

  Planarity restraints: 965
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS H 208 "    0.063 5.00e-02 4.00e+02   9.56e-02 1.46e+01
        pdb=" N   PRO H 209 "   -0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO H 209 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO H 209 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "   -0.046 5.00e-02 4.00e+02   6.80e-02 7.39e+00
        pdb=" N   PRO A 220 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 180 "   -0.042 5.00e-02 4.00e+02   6.38e-02 6.51e+00
        pdb=" N   PRO A 181 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A 181 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 181 "   -0.035 5.00e-02 4.00e+02
  ... (remaining 962 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1142
        2.78 -     3.31: 4982
        3.31 -     3.84: 9209
        3.84 -     4.37: 10533
        4.37 -     4.90: 18948
  Nonbonded interactions: 44814
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  62 "
            pdb=" OG1 THR L  73 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE1 GLN A  68 "
            pdb=" OG  SER A 126 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER H  85 "
            pdb=" OG  SER H  85 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER L 120 "
            pdb=" O   PRO H 132 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NH1 ARG L 107 "
            pdb=" O   ASP L 169 "
     model   vdw
     2.271 3.120
  ... (remaining 44809 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.480
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   5749  Z= 0.180
  Angle     :  0.596  10.026   7817  Z= 0.317
  Chirality :  0.040   0.134    908
  Planarity :  0.006   0.096    965
  Dihedral  : 16.431  81.730   2062
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 27.79 %
    Favored  : 67.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.59 (0.32), residues: 728
  helix:  1.93 (0.34), residues: 258
  sheet:  0.27 (0.38), residues: 198
  loop : -1.02 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.018   0.001   PHE H 155 
 TYR   0.012   0.001   TYR H 184 
 ARG   0.002   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 72
  time to evaluate  : 0.573 
Fit side-chains
REVERT: L    4 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7425 (mtp)
REVERT: H  107 PHE cc_start: 0.6643 (OUTLIER) cc_final: 0.6248 (p90)
  outliers start: 29
  outliers final: 25
  residues processed: 98
  average time/residue: 0.1433
  time to fit residues: 19.7632
Evaluate side-chains
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 ILE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  120 ILE
Chi-restraints excluded: chain A residue  126 SER
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  199 SER
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  246 LEU
Chi-restraints excluded: chain A residue  256 MET
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   24 SER
Chi-restraints excluded: chain L residue   71 SER
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  176 SER
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   76 SER
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  110 ASP
Chi-restraints excluded: chain H residue  117 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 29 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.182534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.141632 restraints weight = 6095.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.90
r_work: 0.2945 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.0649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5749  Z= 0.218
  Angle     :  0.553   8.073   7817  Z= 0.283
  Chirality :  0.042   0.148    908
  Planarity :  0.006   0.067    965
  Dihedral  :  8.357  69.429    822
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 27.00 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.79 (0.33), residues: 728
  helix:  2.00 (0.33), residues: 266
  sheet:  0.26 (0.36), residues: 221
  loop : -0.84 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  90 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.013   0.001   TYR H 154 
 ARG   0.002   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 79
  time to evaluate  : 0.612 
Fit side-chains
REVERT: A  257 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: L    4 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8015 (mtp)
REVERT: L  107 ARG cc_start: 0.8026 (ptm160) cc_final: 0.7690 (ptm160)
  outliers start: 32
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1449
  time to fit residues: 20.9156
Evaluate side-chains
  96 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   24 SER
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue  131 VAL
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  205 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.180969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.120931 restraints weight = 6119.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.17
r_work: 0.2859 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.0937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5749  Z= 0.238
  Angle     :  0.549   6.615   7817  Z= 0.281
  Chirality :  0.041   0.147    908
  Planarity :  0.005   0.060    965
  Dihedral  :  7.024  69.492    796
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.16 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.78 (0.33), residues: 728
  helix:  1.98 (0.32), residues: 266
  sheet:  0.25 (0.36), residues: 221
  loop : -0.84 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP L  90 
 HIS   0.002   0.001   HIS L  88 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.013   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A 252 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 74
  time to evaluate  : 0.603 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2290 (tmt) cc_final: 0.1793 (ttt)
REVERT: A  196 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7713 (tm)
REVERT: A  257 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8258 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1419
  time to fit residues: 19.4159
Evaluate side-chains
  94 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  170 CYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue  131 VAL
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  205 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0770
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.1742

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

Flipped N/Q/H residues before XYZ refinement:
L  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.180157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.119572 restraints weight = 6196.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.11
r_work: 0.2851 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5749  Z= 0.250
  Angle     :  0.551   7.311   7817  Z= 0.282
  Chirality :  0.041   0.150    908
  Planarity :  0.005   0.055    965
  Dihedral  :  6.308  69.509    789
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 26.06 %
    Favored  : 69.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.76 (0.32), residues: 728
  helix:  1.99 (0.32), residues: 266
  sheet:  0.22 (0.36), residues: 221
  loop : -0.86 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP L  90 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A 252 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2358 (tmt) cc_final: 0.1905 (ttt)
REVERT: A  257 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: L  107 ARG cc_start: 0.8070 (ptm160) cc_final: 0.7669 (ptm160)
  outliers start: 31
  outliers final: 25
  residues processed: 102
  average time/residue: 0.1367
  time to fit residues: 19.8271
Evaluate side-chains
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  218 MET
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   84 SER
Chi-restraints excluded: chain L residue  131 VAL
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue   55 ASN
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue   98 ILE
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  205 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 63 optimal weight:    0.0980
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
L  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.174087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.136460 restraints weight = 6000.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.51
r_work: 0.2844 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.162
  Angle     :  0.520   8.385   7817  Z= 0.263
  Chirality :  0.040   0.147    908
  Planarity :  0.005   0.050    965
  Dihedral  :  6.053  69.613    789
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 27.79 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.86 (0.33), residues: 728
  helix:  2.14 (0.33), residues: 266
  sheet:  0.18 (0.36), residues: 223
  loop : -0.78 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.009   0.001   PHE H 107 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2598 (tmt) cc_final: 0.1981 (ttt)
REVERT: A  196 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7692 (tm)
REVERT: A  257 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8073 (tm-30)
REVERT: L  174 MET cc_start: 0.8174 (tpt) cc_final: 0.7755 (tpt)
REVERT: H    5 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7478 (tt0)
  outliers start: 21
  outliers final: 13
  residues processed: 93
  average time/residue: 0.1391
  time to fit residues: 18.2284
Evaluate side-chains
  89 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain L residue  131 VAL
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  186 LEU
Chi-restraints excluded: chain H residue  205 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 68 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
L  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.166805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.122291 restraints weight = 6075.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 3.28
r_work: 0.2726 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5749  Z= 0.240
  Angle     :  0.552   9.469   7817  Z= 0.279
  Chirality :  0.041   0.149    908
  Planarity :  0.005   0.049    965
  Dihedral  :  5.981  69.686    787
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.84 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.81 (0.33), residues: 728
  helix:  2.08 (0.32), residues: 266
  sheet:  0.21 (0.36), residues: 221
  loop : -0.84 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP L  90 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.013   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A 252 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.514 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2508 (tmt) cc_final: 0.1928 (ttt)
REVERT: A  196 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7627 (tm)
REVERT: A  257 GLU cc_start: 0.8423 (tm-30) cc_final: 0.8150 (tm-30)
REVERT: L  107 ARG cc_start: 0.8113 (ptm160) cc_final: 0.7782 (ptm160)
REVERT: L  174 MET cc_start: 0.8256 (tpt) cc_final: 0.7913 (tpt)
REVERT: H    5 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7583 (tt0)
  outliers start: 29
  outliers final: 19
  residues processed: 103
  average time/residue: 0.1411
  time to fit residues: 20.3345
Evaluate side-chains
  96 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain H residue  206 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0030
   chunk 19 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
L  30 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.181652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.141398 restraints weight = 6074.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.85
r_work: 0.2892 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.1250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.181
  Angle     :  0.538  10.091   7817  Z= 0.271
  Chirality :  0.041   0.153    908
  Planarity :  0.005   0.049    965
  Dihedral  :  5.937  69.826    787
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.47 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.84 (0.33), residues: 728
  helix:  2.10 (0.32), residues: 266
  sheet:  0.23 (0.36), residues: 223
  loop : -0.85 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  90 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.010   0.001   PHE H 107 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6101 (ptt90)
REVERT: A  184 MET cc_start: 0.2462 (tmt) cc_final: 0.1913 (ttt)
REVERT: A  196 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7598 (tm)
REVERT: A  257 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8101 (tm-30)
REVERT: L  107 ARG cc_start: 0.8055 (ptm160) cc_final: 0.7647 (ptm160)
REVERT: H    5 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7482 (tt0)
  outliers start: 26
  outliers final: 19
  residues processed: 99
  average time/residue: 0.1579
  time to fit residues: 21.3760
Evaluate side-chains
  95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  186 LEU
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain H residue  206 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    7.9990
   chunk 28 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0570
   chunk 69 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.3980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.6700

-------------------------------------------------------------------------------
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 = 0.3974 r_free = 0.3974 target = 0.182053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.140202 restraints weight = 6045.978|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.10
r_work: 0.2922 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.182
  Angle     :  0.536  10.593   7817  Z= 0.269
  Chirality :  0.041   0.147    908
  Planarity :  0.005   0.048    965
  Dihedral  :  5.898  69.929    787
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 27.63 %
    Favored  : 68.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.86 (0.33), residues: 728
  helix:  2.14 (0.32), residues: 266
  sheet:  0.22 (0.35), residues: 223
  loop : -0.84 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.010   0.001   PHE H 107 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.621 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6562 (OUTLIER) cc_final: 0.6037 (ptt90)
REVERT: A  184 MET cc_start: 0.2550 (OUTLIER) cc_final: 0.1992 (ttt)
REVERT: A  196 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7608 (tm)
REVERT: A  256 MET cc_start: 0.8010 (mmm) cc_final: 0.7745 (mmm)
REVERT: A  257 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: L  107 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7591 (ptm160)
REVERT: L  174 MET cc_start: 0.8063 (tpt) cc_final: 0.7520 (tpt)
REVERT: H    5 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7472 (tt0)
  outliers start: 25
  outliers final: 20
  residues processed: 97
  average time/residue: 0.1460
  time to fit residues: 19.4273
Evaluate side-chains
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  123 THR
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  186 LEU
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain H residue  206 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 19 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0770
   chunk 9 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.183037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.145015 restraints weight = 6117.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.84
r_work: 0.2938 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.164
  Angle     :  0.531  10.878   7817  Z= 0.267
  Chirality :  0.040   0.147    908
  Planarity :  0.005   0.048    965
  Dihedral  :  5.840  70.095    787
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 28.10 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.90 (0.33), residues: 728
  helix:  2.18 (0.32), residues: 266
  sheet:  0.25 (0.35), residues: 223
  loop : -0.85 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.014   0.001   PHE A  37 
 TYR   0.027   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.6139 (ptt90)
REVERT: A  184 MET cc_start: 0.2520 (OUTLIER) cc_final: 0.1980 (ttt)
REVERT: A  196 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7616 (tm)
REVERT: A  256 MET cc_start: 0.8124 (mmm) cc_final: 0.7887 (mmm)
REVERT: A  257 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: L  107 ARG cc_start: 0.8078 (ptm160) cc_final: 0.7635 (ptm160)
REVERT: L  174 MET cc_start: 0.8284 (tpt) cc_final: 0.7774 (tpt)
REVERT: H    5 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7562 (tt0)
  outliers start: 21
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1488
  time to fit residues: 19.4779
Evaluate side-chains
  95 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  186 LEU
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain H residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0980
   chunk 65 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3978 r_free = 0.3978 target = 0.182228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.140475 restraints weight = 6136.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.86
r_work: 0.2905 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.1416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.194
  Angle     :  0.547  11.348   7817  Z= 0.275
  Chirality :  0.041   0.147    908
  Planarity :  0.005   0.047    965
  Dihedral  :  5.825  70.169    787
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 28.10 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.87 (0.32), residues: 728
  helix:  2.16 (0.32), residues: 266
  sheet:  0.27 (0.35), residues: 223
  loop : -0.91 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.011   0.001   PHE A  37 
 TYR   0.029   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A  21 

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.646 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6504 (OUTLIER) cc_final: 0.5989 (ptt90)
REVERT: A  184 MET cc_start: 0.2521 (OUTLIER) cc_final: 0.1996 (ttt)
REVERT: A  196 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7567 (tm)
REVERT: A  257 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: L  107 ARG cc_start: 0.8022 (ptm160) cc_final: 0.7564 (ptm160)
REVERT: L  174 MET cc_start: 0.8098 (tpt) cc_final: 0.7507 (tpt)
REVERT: H    5 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7466 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 95
  average time/residue: 0.1488
  time to fit residues: 19.3961
Evaluate side-chains
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 PHE
Chi-restraints excluded: chain A residue   71 ILE
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  129 CYS
Chi-restraints excluded: chain A residue  143 ARG
Chi-restraints excluded: chain A residue  184 MET
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue  171 THR
Chi-restraints excluded: chain L residue  192 THR
Chi-restraints excluded: chain H residue    5 GLN
Chi-restraints excluded: chain H residue   50 GLU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain H residue  107 PHE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain H residue  129 SER
Chi-restraints excluded: chain H residue  186 LEU
Chi-restraints excluded: chain H residue  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
Chi-restraints excluded: chain H residue  206 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0670
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.6522

-------------------------------------------------------------------------------
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 = 0.3981 r_free = 0.3981 target = 0.182719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.142978 restraints weight = 6127.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.67
r_work: 0.2956 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.1443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5749  Z= 0.180
  Angle     :  0.541  11.094   7817  Z= 0.272
  Chirality :  0.040   0.145    908
  Planarity :  0.005   0.047    965
  Dihedral  :  5.766  70.282    787
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 28.41 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.20 %
    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:  0.89 (0.32), residues: 728
  helix:  2.19 (0.32), residues: 266
  sheet:  0.28 (0.35), residues: 223
  loop : -0.91 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP L 162 
 HIS   0.002   0.001   HIS L  33 
 PHE   0.011   0.001   PHE A  37 
 TYR   0.029   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2965.37 seconds
wall clock time: 53 minutes 29.66 seconds (3209.66 seconds total)