Starting phenix.real_space_refine
on Thu Jul 24 07:05:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fci_31526/07_2025/7fci_31526.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fci_31526/07_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_31526/07_2025/7fci_31526.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fci_31526/07_2025/7fci_31526.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fci_31526/07_2025/7fci_31526.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fci_31526/07_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-5711/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: 4.19, per 1000 atoms: 0.75
  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: 1.43
  Conformation dependent library (CDL) restraints added in 716.9 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: 0.72
  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: 1.75

  Time building geometry restraints manager: 1.72 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:             0.980
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.290
  Find NCS groups from input model:        0.230
  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:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.630
-------------------------------------------------------------------------------
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   5753  Z= 0.129
  Angle     :  0.595  10.026   7825  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13444 (  319)
  hydrogen bonds       : angle       6.28372 (  915)
  SS BOND              : bond        0.00244 (    4)
  SS BOND              : angle       0.42806 (    8)
  covalent geometry    : bond        0.00287 ( 5749)
  covalent geometry    : angle       0.59559 ( 7817)

*********************** 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  : 0.599 
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: 0.1266
  time to fit residues: 17.6917
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  : 0.590 
-------------------------------------------------------------------------------
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 = 6095.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.90
r_work: 0.2947 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
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   5753  Z= 0.144
  Angle     :  0.552   8.073   7825  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03847 (  319)
  hydrogen bonds       : angle       4.66262 (  915)
  SS BOND              : bond        0.00288 (    4)
  SS BOND              : angle       0.49321 (    8)
  covalent geometry    : bond        0.00336 ( 5749)
  covalent geometry    : angle       0.55251 ( 7817)

*********************** 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  : 0.654 
Fit side-chains
REVERT: A  257 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: L    4 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8016 (mtp)
REVERT: L  107 ARG cc_start: 0.8025 (ptm160) cc_final: 0.7687 (ptm160)
  outliers start: 32
  outliers final: 20
  residues processed: 105
  average time/residue: 0.1418
  time to fit residues: 20.5905
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  : 0.643 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 57 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.181148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.120348 restraints weight = 6120.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.16
r_work: 0.2920 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5753  Z= 0.152
  Angle     :  0.547   7.173   7825  Z= 0.280
  Chirality :  0.041   0.147    908
  Planarity :  0.005   0.060    965
  Dihedral  :  7.012  69.508    796
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 27.16 %
    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:  0.80 (0.33), residues: 728
  helix:  2.00 (0.32), residues: 266
  sheet:  0.26 (0.36), residues: 221
  loop : -0.83 (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  88 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.013   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  319)
  hydrogen bonds       : angle       4.45248 (  915)
  SS BOND              : bond        0.00343 (    4)
  SS BOND              : angle       0.47878 (    8)
  covalent geometry    : bond        0.00357 ( 5749)
  covalent geometry    : angle       0.54738 ( 7817)

*********************** 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: 25
    poor density    : 75
  time to evaluate  : 0.604 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2337 (tmt) cc_final: 0.1833 (ttt)
REVERT: A  257 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8258 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1370
  time to fit residues: 18.8251
Evaluate side-chains
  92 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0470
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    5.9990
   chunk 27 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.7280

-------------------------------------------------------------------------------
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 = 0.181750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.120794 restraints weight = 6189.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 2.25
r_work: 0.2915 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2754 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.125
  Angle     :  0.524   7.105   7825  Z= 0.267
  Chirality :  0.040   0.147    908
  Planarity :  0.005   0.053    965
  Dihedral  :  6.183  69.601    789
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 26.84 %
    Favored  : 69.23 %
  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 (0.33), residues: 728
  helix:  2.10 (0.32), residues: 266
  sheet:  0.27 (0.36), residues: 221
  loop : -0.81 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  90 
 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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  319)
  hydrogen bonds       : angle       4.31869 (  915)
  SS BOND              : bond        0.00313 (    4)
  SS BOND              : angle       0.41955 (    8)
  covalent geometry    : bond        0.00288 ( 5749)
  covalent geometry    : angle       0.52430 ( 7817)

*********************** 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
  102 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2403 (tmt) cc_final: 0.1948 (ttt)
REVERT: A  196 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7676 (tm)
REVERT: A  257 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: L  107 ARG cc_start: 0.8032 (ptm160) cc_final: 0.7624 (ptm160)
REVERT: H    5 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7459 (tt0)
  outliers start: 25
  outliers final: 20
  residues processed: 100
  average time/residue: 0.1379
  time to fit residues: 19.3780
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  : 0.652 
-------------------------------------------------------------------------------
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  196 LEU
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   26 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    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
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:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 63 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0770
   chunk 58 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    9.9990
   overall best weight:    0.7738

-------------------------------------------------------------------------------
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 = 0.3872 r_free = 0.3872 target = 0.175235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.135104 restraints weight = 5980.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.42
r_work: 0.2826 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.1102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.129
  Angle     :  0.529   8.176   7825  Z= 0.268
  Chirality :  0.041   0.147    908
  Planarity :  0.005   0.049    965
  Dihedral  :  6.055  69.691    788
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 27.16 %
    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:  0.88 (0.33), residues: 728
  helix:  2.12 (0.32), residues: 266
  sheet:  0.26 (0.36), residues: 221
  loop : -0.81 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 162 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.011   0.001   PHE H 107 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  319)
  hydrogen bonds       : angle       4.27106 (  915)
  SS BOND              : bond        0.00286 (    4)
  SS BOND              : angle       0.38707 (    8)
  covalent geometry    : bond        0.00299 ( 5749)
  covalent geometry    : angle       0.52929 ( 7817)

*********************** 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
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.588 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2600 (tmt) cc_final: 0.2108 (ttt)
REVERT: A  196 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7676 (tm)
REVERT: A  257 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8061 (tm-30)
REVERT: L  174 MET cc_start: 0.8222 (tpt) cc_final: 0.7655 (tpt)
REVERT: H    5 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7428 (tt0)
  outliers start: 27
  outliers final: 19
  residues processed: 98
  average time/residue: 0.1288
  time to fit residues: 17.8274
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  : 0.592 
-------------------------------------------------------------------------------
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  147 ASP
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   22 THR
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   71 THR
Chi-restraints excluded: chain H residue   81 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0870
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.7558

-------------------------------------------------------------------------------
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 = 0.3806 r_free = 0.3806 target = 0.168762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.127580 restraints weight = 6067.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 2.68
r_work: 0.2824 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.130
  Angle     :  0.534   9.596   7825  Z= 0.268
  Chirality :  0.040   0.146    908
  Planarity :  0.005   0.048    965
  Dihedral  :  6.021  69.805    788
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.00 %
    Favored  : 69.23 %
  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 (0.33), residues: 728
  helix:  2.14 (0.32), residues: 266
  sheet:  0.24 (0.36), residues: 221
  loop : -0.83 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 162 
 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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03551 (  319)
  hydrogen bonds       : angle       4.24701 (  915)
  SS BOND              : bond        0.00299 (    4)
  SS BOND              : angle       0.57711 (    8)
  covalent geometry    : bond        0.00303 ( 5749)
  covalent geometry    : angle       0.53382 ( 7817)

*********************** 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
  102 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2575 (tmt) cc_final: 0.1973 (ttt)
REVERT: A  196 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7586 (tm)
REVERT: A  257 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: L  107 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7731 (ptm160)
REVERT: L  174 MET cc_start: 0.8242 (tpt) cc_final: 0.7704 (tpt)
REVERT: H    5 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7479 (tt0)
  outliers start: 24
  outliers final: 19
  residues processed: 101
  average time/residue: 0.1314
  time to fit residues: 18.6460
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  : 0.597 
-------------------------------------------------------------------------------
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  147 ASP
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 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   71 THR
Chi-restraints excluded: chain H residue   81 MET
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   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 = 0.3857 r_free = 0.3857 target = 0.173602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.132790 restraints weight = 6010.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.3379 rms_B_bonded: 2.66
r_work: 0.2854 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.1246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.141
  Angle     :  0.549  10.160   7825  Z= 0.277
  Chirality :  0.041   0.153    908
  Planarity :  0.005   0.048    965
  Dihedral  :  5.965  69.900    787
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 27.16 %
    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:  0.82 (0.33), residues: 728
  helix:  2.08 (0.32), residues: 266
  sheet:  0.21 (0.36), residues: 221
  loop : -0.83 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L 162 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.014   0.001   PHE A  37 
 TYR   0.012   0.001   TYR H 154 
 ARG   0.001   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03673 (  319)
  hydrogen bonds       : angle       4.26930 (  915)
  SS BOND              : bond        0.00559 (    4)
  SS BOND              : angle       0.66741 (    8)
  covalent geometry    : bond        0.00329 ( 5749)
  covalent geometry    : angle       0.54900 ( 7817)

*********************** 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
  104 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A  184 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.1985 (ttt)
REVERT: A  196 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7614 (tm)
REVERT: A  257 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8093 (tm-30)
REVERT: L  107 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7668 (ptm160)
REVERT: L  174 MET cc_start: 0.8233 (tpt) cc_final: 0.7750 (tpt)
REVERT: H    5 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7531 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 101
  average time/residue: 0.1437
  time to fit residues: 20.6562
Evaluate side-chains
  98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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  147 ASP
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  184 MET
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 A residue  240 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   81 MET
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  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 72
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 71 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.2980
   chunk 23 optimal weight:    6.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.180973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.120287 restraints weight = 6065.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.02
r_work: 0.2876 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5753  Z= 0.149
  Angle     :  0.555  10.474   7825  Z= 0.280
  Chirality :  0.041   0.148    908
  Planarity :  0.005   0.048    965
  Dihedral  :  5.971  69.918    787
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.32 %
    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:  0.76 (0.32), residues: 728
  helix:  2.03 (0.32), residues: 266
  sheet:  0.21 (0.35), residues: 223
  loop : -0.90 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP L  90 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.011   0.001   PHE H 107 
 TYR   0.030   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  319)
  hydrogen bonds       : angle       4.26505 (  915)
  SS BOND              : bond        0.00365 (    4)
  SS BOND              : angle       0.62397 (    8)
  covalent geometry    : bond        0.00350 ( 5749)
  covalent geometry    : angle       0.55515 ( 7817)

*********************** 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
  103 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6525 (OUTLIER) cc_final: 0.5952 (ptt90)
REVERT: A  184 MET cc_start: 0.2480 (tmt) cc_final: 0.1942 (ttt)
REVERT: A  196 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7558 (tm)
REVERT: A  256 MET cc_start: 0.8108 (mmm) cc_final: 0.7813 (mmm)
REVERT: A  257 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8132 (tm-30)
REVERT: L  107 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7605 (ptm160)
REVERT: L  174 MET cc_start: 0.8185 (tpt) cc_final: 0.7730 (tpt)
REVERT: H    5 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7497 (tt0)
  outliers start: 26
  outliers final: 23
  residues processed: 99
  average time/residue: 0.1468
  time to fit residues: 20.2758
Evaluate side-chains
  102 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
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  167 LEU
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 A residue  240 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   81 MET
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  192 VAL
Chi-restraints excluded: chain H residue  205 ASN
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:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 35 optimal weight:    0.3980
   chunk 9 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3808 r_free = 0.3808 target = 0.168749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.107140 restraints weight = 6074.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.02
r_work: 0.2896 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.120
  Angle     :  0.537  11.099   7825  Z= 0.270
  Chirality :  0.040   0.147    908
  Planarity :  0.005   0.048    965
  Dihedral  :  5.868  70.040    787
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 27.94 %
    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:  0.83 (0.33), residues: 728
  helix:  2.12 (0.32), residues: 266
  sheet:  0.23 (0.35), residues: 223
  loop : -0.89 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L 162 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.010   0.001   PHE H 107 
 TYR   0.027   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  319)
  hydrogen bonds       : angle       4.18686 (  915)
  SS BOND              : bond        0.00327 (    4)
  SS BOND              : angle       0.41060 (    8)
  covalent geometry    : bond        0.00275 ( 5749)
  covalent geometry    : angle       0.53698 ( 7817)

*********************** 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
  99 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.689 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5977 (ptt90)
REVERT: A  196 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7553 (tm)
REVERT: A  256 MET cc_start: 0.8120 (mmm) cc_final: 0.7829 (mmm)
REVERT: A  257 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: L  107 ARG cc_start: 0.8027 (ptm160) cc_final: 0.7588 (ptm160)
REVERT: L  174 MET cc_start: 0.8193 (tpt) cc_final: 0.7748 (tpt)
REVERT: H    5 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7528 (tt0)
  outliers start: 24
  outliers final: 18
  residues processed: 96
  average time/residue: 0.1534
  time to fit residues: 20.3227
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  : 0.616 
-------------------------------------------------------------------------------
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  143 ARG
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  200 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   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
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:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.167255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.129173 restraints weight = 6123.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 2.68
r_work: 0.2781 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5753  Z= 0.157
  Angle     :  0.570  11.413   7825  Z= 0.286
  Chirality :  0.041   0.150    908
  Planarity :  0.005   0.047    965
  Dihedral  :  5.917  69.994    787
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.56
  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:  0.73 (0.32), residues: 728
  helix:  2.00 (0.32), residues: 266
  sheet:  0.20 (0.35), residues: 223
  loop : -0.93 (0.41), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP L  90 
 HIS   0.003   0.001   HIS L  33 
 PHE   0.012   0.001   PHE H 107 
 TYR   0.032   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03774 (  319)
  hydrogen bonds       : angle       4.26679 (  915)
  SS BOND              : bond        0.00386 (    4)
  SS BOND              : angle       0.44223 (    8)
  covalent geometry    : bond        0.00373 ( 5749)
  covalent geometry    : angle       0.56995 ( 7817)

********************** 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
  101 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A  143 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6162 (ptt90)
REVERT: A  256 MET cc_start: 0.8210 (mmm) cc_final: 0.7919 (mmm)
REVERT: A  257 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8134 (tm-30)
REVERT: L  107 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7679 (ptm160)
REVERT: L  174 MET cc_start: 0.8303 (tpt) cc_final: 0.7897 (tpt)
REVERT: H    5 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7565 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 98
  average time/residue: 0.1443
  time to fit residues: 19.5669
Evaluate side-chains
  98 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
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  143 ARG
Chi-restraints excluded: chain A residue  147 ASP
Chi-restraints excluded: chain A residue  200 VAL
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
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:    8.9990
   chunk 23 optimal weight:    0.0970
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.169537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.130696 restraints weight = 6088.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.48
r_work: 0.2858 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5753  Z= 0.147
  Angle     :  0.580  11.225   7825  Z= 0.286
  Chirality :  0.041   0.149    908
  Planarity :  0.005   0.047    965
  Dihedral  :  5.906  70.011    787
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.38
  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:  0.71 (0.32), residues: 728
  helix:  1.96 (0.32), residues: 266
  sheet:  0.21 (0.35), residues: 223
  loop : -0.94 (0.41), 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   0.012   0.001   PHE H 107 
 TYR   0.033   0.001   TYR L  31 
 ARG   0.001   0.000   ARG A 252 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  319)
  hydrogen bonds       : angle       4.26550 (  915)
  SS BOND              : bond        0.00370 (    4)
  SS BOND              : angle       0.41753 (    8)
  covalent geometry    : bond        0.00344 ( 5749)
  covalent geometry    : angle       0.58062 ( 7817)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3205.84 seconds
wall clock time: 55 minutes 43.63 seconds (3343.63 seconds total)