Starting phenix.real_space_refine
on Fri May  9 13:18:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mqh_48524/05_2025/9mqh_48524.cif"
  }
  resolution = 3.9
  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=   0.037
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      21      5.16       5
     C    1379      2.51       5
     N     329      2.21       5
     O     345      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 2074
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2074
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2074
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 52}
          Link IDs: {'PTRANS': 9, 'TRANS': 271}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 198
          Unresolved non-hydrogen angles: 246
          Unresolved non-hydrogen dihedrals: 168
          Unresolved non-hydrogen chiralities: 16
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 106
  Time building chain proxies: 2.30, per 1000 atoms: 1.11
  Number of scatterers: 2074
  At special positions: 0
  Unit cell: (64.295, 57.615, 78.49, 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      21     16.00
     O     345      8.00
     N     329      7.00
     C    1379      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 219 " 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: 0.52
  Conformation dependent library (CDL) restraints added in 265.5 milliseconds
  

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  544

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 1 sheets defined
      87.5% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 97
      removed outlier: 3.914A  pdb=" N   LEU A  90 " --> pdb=" O   PHE A  86 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A  96 " --> pdb=" O   MET A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.535A  pdb=" N   LYS A 102 " --> pdb=" O   THR A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 122
      removed outlier: 3.690A  pdb=" N   ILE A 107 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TYR A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   THR A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 129
      removed outlier: 3.878A  pdb=" N   ASN A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 173
      removed outlier: 3.883A  pdb=" N   MET A 153 " --> pdb=" O   ASP A 149 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   PHE A 154 " --> pdb=" O   TYR A 150 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE A 157 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 4.070A  pdb=" N   ASP A 179 " --> pdb=" O   VAL A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 187 through 208
      removed outlier: 3.980A  pdb=" N   VAL A 191 " --> pdb=" O   LYS A 187 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA A 199 " --> pdb=" O   ILE A 195 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ILE A 200 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      Proline residue:  A 203  - end of helix
      removed outlier: 3.505A  pdb=" N   ALA A 208 " --> pdb=" O   VAL A 204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 243
      removed outlier: 3.855A  pdb=" N   LYS A 235 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 262
    Processing helix  chain 'A' and resid 270 through 309
      removed outlier: 4.230A  pdb=" N   ARG A 275 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
      removed outlier: 4.622A  pdb=" N   ASN A 276 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.598A  pdb=" N   ILE A 300 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 338
      removed outlier: 3.864A  pdb=" N   ASN A 330 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   SER A 331 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   CYS A 332 " --> pdb=" O   TYR A 328 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ASN A 334 " --> pdb=" O   ASN A 330 " (cutoff:3.500A)
      Proline residue:  A 335  - end of helix
    Processing helix  chain 'A' and resid 342 through 354
      removed outlier: 3.708A  pdb=" N   ARG A 350 " --> pdb=" O   LYS A 346 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212

    162 hydrogen bonds defined for protein.
    480 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: 0.51

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 624
        1.35 -     1.46: 544
        1.46 -     1.58: 926
        1.58 -     1.70: 0
        1.70 -     1.81: 30
  Bond restraints: 2124
  Sorted by residual:
  bond pdb=" CG  LEU A 202 "
       pdb=" CD2 LEU A 202 "
    ideal  model  delta    sigma   weight residual
    1.521  1.498  0.023 3.30e-02 9.18e+02 5.03e-01
  bond pdb=" C   PHE A 137 "
       pdb=" N   GLY A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.330 -0.009 1.24e-02 6.50e+03 4.80e-01
  bond pdb=" CB  ILE A 169 "
       pdb=" CG2 ILE A 169 "
    ideal  model  delta    sigma   weight residual
    1.521  1.499  0.022 3.30e-02 9.18e+02 4.56e-01
  bond pdb=" CG  MET A 257 "
       pdb=" SD  MET A 257 "
    ideal  model  delta    sigma   weight residual
    1.803  1.788  0.015 2.50e-02 1.60e+03 3.63e-01
  bond pdb=" C   LEU A 123 "
       pdb=" N   PRO A 124 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.007 1.28e-02 6.10e+03 3.25e-01
  ... (remaining 2119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 2800
        1.24 -     2.48: 91
        2.48 -     3.73: 14
        3.73 -     4.97: 8
        4.97 -     6.21: 2
  Bond angle restraints: 2915
  Sorted by residual:
  angle pdb=" N   MET A 132 "
        pdb=" CA  MET A 132 "
        pdb=" C   MET A 132 "
      ideal   model   delta    sigma   weight residual
     113.43  110.58    2.85 1.26e+00 6.30e-01 5.13e+00
  angle pdb=" CA  GLY A 138 "
        pdb=" C   GLY A 138 "
        pdb=" N   THR A 139 "
      ideal   model   delta    sigma   weight residual
     115.34  117.01   -1.67 8.40e-01 1.42e+00 3.93e+00
  angle pdb=" CA  LEU A  90 "
        pdb=" CB  LEU A  90 "
        pdb=" CG  LEU A  90 "
      ideal   model   delta    sigma   weight residual
     116.30  122.51   -6.21 3.50e+00 8.16e-02 3.15e+00
  angle pdb=" CB  MET A 207 "
        pdb=" CG  MET A 207 "
        pdb=" SD  MET A 207 "
      ideal   model   delta    sigma   weight residual
     112.70  117.75   -5.05 3.00e+00 1.11e-01 2.84e+00
  angle pdb=" CA  GLY A 138 "
        pdb=" C   GLY A 138 "
        pdb=" O   GLY A 138 "
      ideal   model   delta    sigma   weight residual
     122.14  120.41    1.73 1.05e+00 9.07e-01 2.70e+00
  ... (remaining 2910 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.00: 1010
       12.00 -    24.00: 127
       24.00 -    35.99: 62
       35.99 -    47.99: 23
       47.99 -    59.99: 5
  Dihedral angle restraints: 1227
    sinusoidal: 393
      harmonic: 834
  Sorted by residual:
  dihedral pdb=" CA  PHE A 243 "
           pdb=" C   PHE A 243 "
           pdb=" N   ILE A 244 "
           pdb=" CA  ILE A 244 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.56  -15.44     0      5.00e+00 4.00e-02 9.54e+00
  dihedral pdb=" CA  ILE A 107 "
           pdb=" CB  ILE A 107 "
           pdb=" CG1 ILE A 107 "
           pdb=" CD1 ILE A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.01   59.99     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   TYR A 130 "
           pdb=" CA  TYR A 130 "
           pdb=" CB  TYR A 130 "
           pdb=" CG  TYR A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.46   55.46     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 224
       0.030 -    0.060: 96
       0.060 -    0.090: 34
       0.090 -    0.120: 10
       0.120 -    0.149: 4
  Chirality restraints: 368
  Sorted by residual:
  chirality pdb=" CA  LEU A 202 "
            pdb=" N   LEU A 202 "
            pdb=" C   LEU A 202 "
            pdb=" CB  LEU A 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ILE A 310 "
            pdb=" N   ILE A 310 "
            pdb=" C   ILE A 310 "
            pdb=" CB  ILE A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CB  THR A 155 "
            pdb=" CA  THR A 155 "
            pdb=" OG1 THR A 155 "
            pdb=" CG2 THR A 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.12 2.00e-01 2.50e+01 3.77e-01
  ... (remaining 365 not shown)

  Planarity restraints: 352
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 151 "    0.005 2.00e-02 2.50e+03   9.68e-03 9.37e-01
        pdb=" C   TYR A 151 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   TYR A 151 "    0.006 2.00e-02 2.50e+03
        pdb=" N   ASN A 152 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 173 "   -0.014 5.00e-02 4.00e+02   2.12e-02 7.21e-01
        pdb=" N   PRO A 174 "    0.037 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 334 "   -0.013 5.00e-02 4.00e+02   1.98e-02 6.28e-01
        pdb=" N   PRO A 335 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A 335 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 335 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 349 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 267
        2.74 -     3.28: 2118
        3.28 -     3.82: 3498
        3.82 -     4.36: 3427
        4.36 -     4.90: 6293
  Nonbonded interactions: 15603
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  84 "
            pdb=" ND2 ASN A  88 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   LEU A 118 "
            pdb=" OG  SER A 121 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG1 THR A 122 "
            pdb=" OE1 GLN A 126 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   LEU A 123 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" NE1 TRP A 135 "
            pdb=" O   GLY A 138 "
     model   vdw
     2.346 3.120
  ... (remaining 15598 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.920
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     10.510
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
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   0.023   2125  Z= 0.140
  Angle     :  0.588   6.211   2917  Z= 0.317
  Chirality :  0.040   0.149    368
  Planarity :  0.003   0.026    352
  Dihedral  : 15.160  59.987    680
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 26.47 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.53), residues: 277
  helix:  1.72 (0.36), residues: 206
  sheet:  None (None), residues: 0
  loop : -1.44 (0.86), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 295 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.007   0.001   PHE A 243 
 TYR   0.011   0.001   TYR A 130 
 ARG   0.002   0.000   ARG A 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17443 (  162)
  hydrogen bonds       : angle       5.28601 (  480)
  SS BOND              : bond        0.00153 (    1)
  SS BOND              : angle       0.51574 (    2)
  covalent geometry    : bond        0.00315 ( 2124)
  covalent geometry    : angle       0.58842 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.4392 (OUTLIER) cc_final: 0.3633 (t80)
REVERT: A  140 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7793 (tt)
REVERT: A  189 ILE cc_start: 0.8809 (mm) cc_final: 0.8431 (mm)
  outliers start: 8
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0720
  time to fit residues: 4.9514
Evaluate side-chains
  55 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  310 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 14 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.144245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124433 restraints weight = 3924.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.127107 restraints weight = 2121.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.128779 restraints weight = 1443.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.021   2125  Z= 0.155
  Angle     :  0.567   5.042   2917  Z= 0.300
  Chirality :  0.041   0.146    368
  Planarity :  0.004   0.031    352
  Dihedral  :  7.458  58.176    309
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  8.82 %
    Allowed  : 21.08 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.53), residues: 277
  helix:  2.00 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.67 (0.89), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.019   0.001   PHE A  89 
 TYR   0.011   0.001   TYR A 130 
 ARG   0.002   0.001   ARG A 181 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04830 (  162)
  hydrogen bonds       : angle       3.87176 (  480)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       0.58178 (    2)
  covalent geometry    : bond        0.00353 ( 2124)
  covalent geometry    : angle       0.56720 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7892 (mtp)
REVERT: A  130 TYR cc_start: 0.4238 (OUTLIER) cc_final: 0.3280 (t80)
REVERT: A  140 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7797 (tt)
REVERT: A  189 ILE cc_start: 0.8856 (mm) cc_final: 0.8491 (mm)
REVERT: A  207 MET cc_start: 0.8469 (mpp) cc_final: 0.8125 (mpp)
REVERT: A  331 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8454 (p)
REVERT: A  332 CYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7977 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 64
  average time/residue: 0.0863
  time to fit residues: 7.0556
Evaluate side-chains
  61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  329 THR
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  332 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.144276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.124436 restraints weight = 3926.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.126955 restraints weight = 2140.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.128870 restraints weight = 1473.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2125  Z= 0.147
  Angle     :  0.543   4.921   2917  Z= 0.289
  Chirality :  0.040   0.132    368
  Planarity :  0.003   0.022    352
  Dihedral  :  7.255  58.658    306
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 21.08 %
    Favored  : 69.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.53), residues: 277
  helix:  2.08 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.62 (0.89), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.006   0.001   PHE A 158 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.005   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  162)
  hydrogen bonds       : angle       3.68814 (  480)
  SS BOND              : bond        0.00167 (    1)
  SS BOND              : angle       0.54408 (    2)
  covalent geometry    : bond        0.00340 ( 2124)
  covalent geometry    : angle       0.54337 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 47
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7816 (mtp)
REVERT: A  130 TYR cc_start: 0.4225 (OUTLIER) cc_final: 0.3059 (t80)
REVERT: A  140 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7705 (tt)
REVERT: A  189 ILE cc_start: 0.8865 (mm) cc_final: 0.8502 (mm)
REVERT: A  207 MET cc_start: 0.8451 (mpp) cc_final: 0.8170 (mpp)
REVERT: A  331 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (p)
REVERT: A  338 TYR cc_start: 0.8648 (m-10) cc_final: 0.8245 (m-10)
  outliers start: 19
  outliers final: 10
  residues processed: 61
  average time/residue: 0.0716
  time to fit residues: 5.7594
Evaluate side-chains
  60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  331 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.144755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125333 restraints weight = 3975.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127867 restraints weight = 2137.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.129764 restraints weight = 1477.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2125  Z= 0.141
  Angle     :  0.535   5.034   2917  Z= 0.284
  Chirality :  0.040   0.146    368
  Planarity :  0.003   0.022    352
  Dihedral  :  6.349  49.844    305
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  8.82 %
    Allowed  : 23.04 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.54), residues: 277
  helix:  2.24 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -1.27 (0.91), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.006   0.001   PHE A 158 
 TYR   0.010   0.001   TYR A 130 
 ARG   0.004   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04366 (  162)
  hydrogen bonds       : angle       3.58091 (  480)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.54674 (    2)
  covalent geometry    : bond        0.00326 ( 2124)
  covalent geometry    : angle       0.53525 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 48
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7761 (mtp)
REVERT: A  130 TYR cc_start: 0.3829 (OUTLIER) cc_final: 0.2713 (t80)
REVERT: A  140 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7673 (tt)
REVERT: A  189 ILE cc_start: 0.8860 (mm) cc_final: 0.8494 (mm)
REVERT: A  207 MET cc_start: 0.8453 (mpp) cc_final: 0.8213 (mpp)
REVERT: A  331 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8602 (p)
REVERT: A  338 TYR cc_start: 0.8675 (m-10) cc_final: 0.8264 (m-10)
  outliers start: 18
  outliers final: 12
  residues processed: 60
  average time/residue: 0.0658
  time to fit residues: 5.3024
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  219 CYS
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Chi-restraints excluded: chain A residue  331 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.147340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.128049 restraints weight = 4057.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.130776 restraints weight = 2155.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.132678 restraints weight = 1464.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2125  Z= 0.117
  Angle     :  0.502   4.811   2917  Z= 0.271
  Chirality :  0.039   0.161    368
  Planarity :  0.003   0.021    352
  Dihedral  :  6.166  45.007    305
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 25.98 %
    Favored  : 65.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.54), residues: 277
  helix:  2.29 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -0.98 (0.93), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.007   0.001   PHE A  89 
 TYR   0.009   0.001   TYR A 254 
 ARG   0.003   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  162)
  hydrogen bonds       : angle       3.42098 (  480)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.53997 (    2)
  covalent geometry    : bond        0.00263 ( 2124)
  covalent geometry    : angle       0.50190 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7717 (mtp)
REVERT: A  130 TYR cc_start: 0.3801 (OUTLIER) cc_final: 0.2768 (t80)
REVERT: A  140 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7632 (tt)
REVERT: A  189 ILE cc_start: 0.8811 (mm) cc_final: 0.8477 (mm)
REVERT: A  338 TYR cc_start: 0.8655 (m-10) cc_final: 0.8202 (m-10)
  outliers start: 17
  outliers final: 12
  residues processed: 62
  average time/residue: 0.0616
  time to fit residues: 5.1369
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  130 TYR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    5.9990
   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 = 0.3797 r_free = 0.3797 target = 0.143411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.123985 restraints weight = 3998.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126539 restraints weight = 2178.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128374 restraints weight = 1500.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   2125  Z= 0.172
  Angle     :  0.576   4.926   2917  Z= 0.310
  Chirality :  0.041   0.156    368
  Planarity :  0.004   0.027    352
  Dihedral  :  6.221  42.656    305
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 25.00 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.53), residues: 277
  helix:  2.08 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.15 (0.90), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.003   0.001   HIS A 299 
 PHE   0.008   0.001   PHE A 158 
 TYR   0.012   0.002   TYR A 130 
 ARG   0.004   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04771 (  162)
  hydrogen bonds       : angle       3.68332 (  480)
  SS BOND              : bond        0.00233 (    1)
  SS BOND              : angle       0.52568 (    2)
  covalent geometry    : bond        0.00404 ( 2124)
  covalent geometry    : angle       0.57637 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7804 (mtp)
REVERT: A  140 ILE cc_start: 0.8118 (OUTLIER) cc_final: 0.7689 (tt)
REVERT: A  189 ILE cc_start: 0.8926 (mm) cc_final: 0.8527 (mm)
REVERT: A  338 TYR cc_start: 0.8657 (m-10) cc_final: 0.8219 (m-10)
  outliers start: 17
  outliers final: 12
  residues processed: 57
  average time/residue: 0.0799
  time to fit residues: 5.9960
Evaluate side-chains
  60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 27 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   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 = 0.3828 r_free = 0.3828 target = 0.146071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126395 restraints weight = 4052.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129045 restraints weight = 2158.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.131036 restraints weight = 1466.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   2125  Z= 0.124
  Angle     :  0.525   4.831   2917  Z= 0.282
  Chirality :  0.040   0.140    368
  Planarity :  0.003   0.021    352
  Dihedral  :  5.676  43.190    303
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 25.49 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.53), residues: 277
  helix:  2.22 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.04 (0.91), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.008   0.001   PHE A  89 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.003   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  162)
  hydrogen bonds       : angle       3.51696 (  480)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.46385 (    2)
  covalent geometry    : bond        0.00281 ( 2124)
  covalent geometry    : angle       0.52463 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7749 (mtp)
REVERT: A  140 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7670 (tt)
REVERT: A  189 ILE cc_start: 0.8857 (mm) cc_final: 0.8488 (mm)
REVERT: A  338 TYR cc_start: 0.8655 (m-10) cc_final: 0.8222 (m-10)
  outliers start: 19
  outliers final: 16
  residues processed: 59
  average time/residue: 0.0669
  time to fit residues: 5.3403
Evaluate side-chains
  64 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  144 ILE
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3825 r_free = 0.3825 target = 0.145574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125981 restraints weight = 4173.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.128853 restraints weight = 2229.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.130234 restraints weight = 1494.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2125  Z= 0.133
  Angle     :  0.541   4.903   2917  Z= 0.291
  Chirality :  0.040   0.138    368
  Planarity :  0.003   0.021    352
  Dihedral  :  5.670  42.900    303
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 26.47 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.53), residues: 277
  helix:  2.17 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -1.01 (0.92), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.006   0.001   PHE A 158 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.004   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04203 (  162)
  hydrogen bonds       : angle       3.54995 (  480)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       0.19780 (    2)
  covalent geometry    : bond        0.00306 ( 2124)
  covalent geometry    : angle       0.54145 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 47
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7759 (mtp)
REVERT: A  140 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7682 (tt)
REVERT: A  189 ILE cc_start: 0.8843 (mm) cc_final: 0.8480 (mm)
REVERT: A  338 TYR cc_start: 0.8646 (m-10) cc_final: 0.8256 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 56
  average time/residue: 0.0668
  time to fit residues: 5.0609
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 7 optimal weight:    0.2980
   chunk 27 optimal weight:    0.0770
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4938

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.147214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.127783 restraints weight = 4069.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.130645 restraints weight = 2168.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132608 restraints weight = 1453.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2125  Z= 0.115
  Angle     :  0.531   6.877   2917  Z= 0.282
  Chirality :  0.039   0.130    368
  Planarity :  0.003   0.020    352
  Dihedral  :  5.565  43.208    303
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 27.45 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.53), residues: 277
  helix:  2.29 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -0.90 (0.92), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.001   0.000   HIS A 299 
 PHE   0.012   0.001   PHE A  89 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.003   0.000   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  162)
  hydrogen bonds       : angle       3.46923 (  480)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.18467 (    2)
  covalent geometry    : bond        0.00258 ( 2124)
  covalent geometry    : angle       0.53114 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7745 (mtp)
REVERT: A  140 ILE cc_start: 0.8057 (OUTLIER) cc_final: 0.7730 (tp)
REVERT: A  189 ILE cc_start: 0.8776 (mm) cc_final: 0.8455 (mm)
REVERT: A  338 TYR cc_start: 0.8622 (m-10) cc_final: 0.8240 (m-10)
  outliers start: 15
  outliers final: 13
  residues processed: 55
  average time/residue: 0.0677
  time to fit residues: 5.0267
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0670
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 19 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 = 0.3832 r_free = 0.3832 target = 0.146025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.126596 restraints weight = 4055.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129262 restraints weight = 2171.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131273 restraints weight = 1474.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2125  Z= 0.129
  Angle     :  0.547   6.226   2917  Z= 0.293
  Chirality :  0.040   0.135    368
  Planarity :  0.003   0.019    352
  Dihedral  :  5.611  42.709    303
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  8.33 %
    Allowed  : 27.45 %
    Favored  : 64.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.53), residues: 277
  helix:  2.13 (0.35), residues: 216
  sheet:  None (None), residues: 0
  loop : -1.30 (0.93), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.005   0.001   PHE A 158 
 TYR   0.011   0.001   TYR A 254 
 ARG   0.003   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  162)
  hydrogen bonds       : angle       3.49819 (  480)
  SS BOND              : bond        0.00210 (    1)
  SS BOND              : angle       0.23174 (    2)
  covalent geometry    : bond        0.00295 ( 2124)
  covalent geometry    : angle       0.54713 ( 2915)

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

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

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  554 Ramachandran restraints generated.
    277 Oldfield, 0 Emsley, 277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7765 (mtp)
REVERT: A  140 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7700 (tp)
REVERT: A  189 ILE cc_start: 0.8810 (mm) cc_final: 0.8466 (mm)
REVERT: A  338 TYR cc_start: 0.8637 (m-10) cc_final: 0.8240 (m-10)
  outliers start: 17
  outliers final: 14
  residues processed: 54
  average time/residue: 0.0661
  time to fit residues: 4.8437
Evaluate side-chains
  62 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 46
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  142 CYS
Chi-restraints excluded: chain A residue  163 MET
Chi-restraints excluded: chain A residue  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  288 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  308 VAL
Chi-restraints excluded: chain A residue  310 ILE
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.144557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124856 restraints weight = 4100.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.127641 restraints weight = 2210.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129373 restraints weight = 1496.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2125  Z= 0.142
  Angle     :  0.556   5.625   2917  Z= 0.298
  Chirality :  0.040   0.137    368
  Planarity :  0.003   0.020    352
  Dihedral  :  5.696  42.637    303
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 27.94 %
    Favored  : 64.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.53), residues: 277
  helix:  2.16 (0.35), residues: 210
  sheet:  None (None), residues: 0
  loop : -0.91 (0.91), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 
 PHE   0.036   0.001   PHE A  89 
 TYR   0.011   0.001   TYR A 130 
 ARG   0.003   0.001   ARG A 278 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04375 (  162)
  hydrogen bonds       : angle       3.55908 (  480)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       0.19730 (    2)
  covalent geometry    : bond        0.00331 ( 2124)
  covalent geometry    : angle       0.55607 ( 2915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1083.34 seconds
wall clock time: 19 minutes 42.88 seconds (1182.88 seconds total)