Starting phenix.real_space_refine
on Wed Sep 17 02:59:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mqh_48524/09_2025/9mqh_48524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mqh_48524/09_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_48524/09_2025/9mqh_48524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mqh_48524/09_2025/9mqh_48524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mqh_48524/09_2025/9mqh_48524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mqh_48524/09_2025/9mqh_48524.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'PHE:plan': 1, 'ARG:plan': 8, 'TYR:plan': 3, 'ASP:plan': 2, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 5}
          Unresolved non-hydrogen planarities: 106
  Time building chain proxies: 0.64, per 1000 atoms: 0.31
  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: 0.16
  Conformation dependent library (CDL) restraints added in 87.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.04
  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: 0.18

  Time building geometry restraints manager: 0.23 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:             2.640
  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:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     3.470
  Find NCS groups from input model:        0.010
  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:1.200
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.390
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A 265 
 TYR   0.011   0.001   TYR A 130 
 PHE   0.007   0.001   PHE A 243 
 TRP   0.003   0.001   TRP A 295 
 HIS   0.002   0.001   HIS A 299 

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

*********************** 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  : 0.081 
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: 0.0306
  time to fit residues: 2.1440
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  : 0.070 
-------------------------------------------------------------------------------
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 27 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 111 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.145353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.125388 restraints weight = 3962.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.128192 restraints weight = 2123.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.129692 restraints weight = 1429.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.131100 restraints weight = 1149.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.131279 restraints weight = 986.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1035

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= 0.140
  Angle     :  0.549   4.810   2917  Z= 0.291
  Chirality :  0.041   0.141    368
  Planarity :  0.004   0.027    352
  Dihedral  :  7.422  57.837    309
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  8.82 %
    Allowed  : 20.10 %
    Favored  : 71.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.53), residues: 277
  helix:  2.05 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.62 (0.90), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 181 
 TYR   0.009   0.001   TYR A 130 
 PHE   0.019   0.001   PHE A  89 
 TRP   0.012   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 2124)
  covalent geometry    : angle       0.54897 ( 2915)
  SS BOND              : bond        0.00206 (    1)
  SS BOND              : angle       0.55171 (    2)
  hydrogen bonds       : bond        0.04599 (  162)
  hydrogen bonds       : angle       3.81245 (  480)

*********************** 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
  71 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7864 (mtp)
REVERT: A  130 TYR cc_start: 0.4299 (OUTLIER) cc_final: 0.3367 (t80)
REVERT: A  140 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7757 (tt)
REVERT: A  189 ILE cc_start: 0.8819 (mm) cc_final: 0.8480 (mm)
REVERT: A  207 MET cc_start: 0.8438 (mpp) cc_final: 0.8116 (mpp)
REVERT: A  331 SER cc_start: 0.8777 (OUTLIER) cc_final: 0.8437 (p)
REVERT: A  332 CYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7956 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 66
  average time/residue: 0.0344
  time to fit residues: 2.9557
Evaluate side-chains
  63 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
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 20 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    0.3980
   chunk 12 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.146403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.126422 restraints weight = 4008.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.129182 restraints weight = 2144.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.130836 restraints weight = 1458.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.132194 restraints weight = 1161.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.132910 restraints weight = 988.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1456

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= 0.120
  Angle     :  0.507   4.767   2917  Z= 0.271
  Chirality :  0.039   0.130    368
  Planarity :  0.003   0.021    352
  Dihedral  :  7.150  57.716    306
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 22.55 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.53), residues: 277
  helix:  2.25 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.53 (0.89), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 278 
 TYR   0.009   0.001   TYR A 254 
 PHE   0.006   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 2124)
  covalent geometry    : angle       0.50728 ( 2915)
  SS BOND              : bond        0.00102 (    1)
  SS BOND              : angle       0.53510 (    2)
  hydrogen bonds       : bond        0.04030 (  162)
  hydrogen bonds       : angle       3.57647 (  480)

*********************** 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
  65 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 49
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7770 (mtp)
REVERT: A  130 TYR cc_start: 0.4301 (OUTLIER) cc_final: 0.3191 (t80)
REVERT: A  140 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: A  189 ILE cc_start: 0.8760 (mm) cc_final: 0.8415 (mm)
REVERT: A  207 MET cc_start: 0.8390 (mpp) cc_final: 0.8142 (mpp)
REVERT: A  331 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8378 (p)
REVERT: A  338 TYR cc_start: 0.8637 (m-10) cc_final: 0.8183 (m-10)
  outliers start: 16
  outliers final: 8
  residues processed: 59
  average time/residue: 0.0271
  time to fit residues: 2.2154
Evaluate side-chains
  58 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
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  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  198 SER
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 8 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3837 r_free = 0.3837 target = 0.146810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.127036 restraints weight = 3953.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.129692 restraints weight = 2140.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131672 restraints weight = 1472.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132514 restraints weight = 1148.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133392 restraints weight = 1011.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1652

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= 0.118
  Angle     :  0.502   4.975   2917  Z= 0.266
  Chirality :  0.039   0.129    368
  Planarity :  0.003   0.020    352
  Dihedral  :  6.740  50.931    306
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 23.04 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.54), residues: 277
  helix:  2.39 (0.35), residues: 208
  sheet:  None (None), residues: 0
  loop : -1.20 (0.91), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.010   0.001   TYR A 254 
 PHE   0.005   0.001   PHE A 158 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 2124)
  covalent geometry    : angle       0.50169 ( 2915)
  SS BOND              : bond        0.00097 (    1)
  SS BOND              : angle       0.52879 (    2)
  hydrogen bonds       : bond        0.03898 (  162)
  hydrogen bonds       : angle       3.46352 (  480)

*********************** 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
  67 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7705 (mtp)
REVERT: A  130 TYR cc_start: 0.4158 (OUTLIER) cc_final: 0.3031 (t80)
REVERT: A  140 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7646 (tt)
REVERT: A  189 ILE cc_start: 0.8755 (mm) cc_final: 0.8435 (mm)
REVERT: A  331 SER cc_start: 0.8824 (OUTLIER) cc_final: 0.8548 (p)
REVERT: A  338 TYR cc_start: 0.8665 (m-10) cc_final: 0.8260 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0276
  time to fit residues: 2.3278
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  : 0.084 
-------------------------------------------------------------------------------
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  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 5 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.144481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124945 restraints weight = 4026.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.127521 restraints weight = 2149.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.129452 restraints weight = 1479.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130389 restraints weight = 1161.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130389 restraints weight = 1014.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.1823

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= 0.144
  Angle     :  0.539   6.442   2917  Z= 0.286
  Chirality :  0.040   0.129    368
  Planarity :  0.003   0.020    352
  Dihedral  :  6.220  46.686    306
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 25.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.17 (0.53), residues: 277
  helix:  2.37 (0.35), residues: 205
  sheet:  None (None), residues: 0
  loop : -1.45 (0.85), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.013   0.001   TYR A 254 
 PHE   0.020   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2124)
  covalent geometry    : angle       0.53875 ( 2915)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.54742 (    2)
  hydrogen bonds       : bond        0.04338 (  162)
  hydrogen bonds       : angle       3.61359 (  480)

*********************** 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
  66 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7765 (mtp)
REVERT: A  130 TYR cc_start: 0.3800 (OUTLIER) cc_final: 0.2748 (t80)
REVERT: A  140 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7658 (tt)
REVERT: A  189 ILE cc_start: 0.8831 (mm) cc_final: 0.8478 (mm)
REVERT: A  338 TYR cc_start: 0.8665 (m-10) cc_final: 0.8205 (m-10)
  outliers start: 16
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0279
  time to fit residues: 2.3540
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  : 0.083 
-------------------------------------------------------------------------------
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  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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.145693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.126062 restraints weight = 3980.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.128590 restraints weight = 2161.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.130589 restraints weight = 1493.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131450 restraints weight = 1169.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.131714 restraints weight = 1026.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1843

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= 0.127
  Angle     :  0.536   4.950   2917  Z= 0.284
  Chirality :  0.040   0.127    368
  Planarity :  0.003   0.020    352
  Dihedral  :  6.120  42.657    305
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 25.98 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.53), residues: 277
  helix:  2.25 (0.35), residues: 207
  sheet:  None (None), residues: 0
  loop : -1.24 (0.87), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 278 
 TYR   0.013   0.001   TYR A 254 
 PHE   0.005   0.001   PHE A 158 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 2124)
  covalent geometry    : angle       0.53619 ( 2915)
  SS BOND              : bond        0.00127 (    1)
  SS BOND              : angle       0.53725 (    2)
  hydrogen bonds       : bond        0.04051 (  162)
  hydrogen bonds       : angle       3.60548 (  480)

*********************** 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: 16
    poor density    : 48
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7740 (mtp)
REVERT: A  140 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7649 (tt)
REVERT: A  189 ILE cc_start: 0.8814 (mm) cc_final: 0.8487 (mm)
REVERT: A  338 TYR cc_start: 0.8663 (m-10) cc_final: 0.8191 (m-10)
  outliers start: 16
  outliers final: 13
  residues processed: 57
  average time/residue: 0.0274
  time to fit residues: 2.1638
Evaluate side-chains
  59 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
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  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0050
   chunk 14 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0070
   chunk 5 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.4412

-------------------------------------------------------------------------------
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 = 0.3836 r_free = 0.3836 target = 0.147000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.127464 restraints weight = 4003.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130324 restraints weight = 2134.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.132009 restraints weight = 1438.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133410 restraints weight = 1137.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133410 restraints weight = 963.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2125  Z= 0.109
  Angle     :  0.510   4.929   2917  Z= 0.271
  Chirality :  0.039   0.127    368
  Planarity :  0.003   0.019    352
  Dihedral  :  5.514  42.872    303
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 26.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.53), residues: 277
  helix:  2.38 (0.35), residues: 207
  sheet:  None (None), residues: 0
  loop : -1.21 (0.87), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 278 
 TYR   0.013   0.001   TYR A 254 
 PHE   0.021   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.001   0.000   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 2124)
  covalent geometry    : angle       0.51008 ( 2915)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.49441 (    2)
  hydrogen bonds       : bond        0.03633 (  162)
  hydrogen bonds       : angle       3.51849 (  480)

*********************** 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
  63 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (mtp)
REVERT: A  140 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7629 (tt)
REVERT: A  189 ILE cc_start: 0.8745 (mm) cc_final: 0.8434 (mm)
REVERT: A  331 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8426 (p)
REVERT: A  338 TYR cc_start: 0.8654 (m-10) cc_final: 0.8241 (m-10)
  outliers start: 16
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0279
  time to fit residues: 2.2396
Evaluate side-chains
  60 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
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  171 VAL
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  196 LEU
Chi-restraints excluded: chain A residue  209 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  308 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3813 r_free = 0.3813 target = 0.144503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.125396 restraints weight = 4052.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127999 restraints weight = 2160.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.130043 restraints weight = 1466.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.130908 restraints weight = 1131.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131275 restraints weight = 989.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2125  Z= 0.148
  Angle     :  0.553   5.031   2917  Z= 0.295
  Chirality :  0.040   0.127    368
  Planarity :  0.003   0.019    352
  Dihedral  :  5.648  42.436    303
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.52), residues: 277
  helix:  2.09 (0.35), residues: 213
  sheet:  None (None), residues: 0
  loop : -1.56 (0.87), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 278 
 TYR   0.011   0.001   TYR A 130 
 PHE   0.007   0.001   PHE A 158 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 2124)
  covalent geometry    : angle       0.55313 ( 2915)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       0.24749 (    2)
  hydrogen bonds       : bond        0.04355 (  162)
  hydrogen bonds       : angle       3.65781 (  480)

*********************** 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
  65 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 48
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7749 (mtp)
REVERT: A  140 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7684 (tt)
REVERT: A  189 ILE cc_start: 0.8856 (mm) cc_final: 0.8501 (mm)
REVERT: A  331 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8462 (p)
REVERT: A  338 TYR cc_start: 0.8674 (m-10) cc_final: 0.8211 (m-10)
  outliers start: 17
  outliers final: 12
  residues processed: 59
  average time/residue: 0.0273
  time to fit residues: 2.2344
Evaluate side-chains
  59 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 44
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
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  122 THR
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  252 VAL
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
Chi-restraints excluded: chain A residue  308 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 28
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0270
   chunk 0 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 = 0.3829 r_free = 0.3829 target = 0.146248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.126775 restraints weight = 4049.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.129433 restraints weight = 2159.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.131561 restraints weight = 1476.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.132248 restraints weight = 1139.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.133111 restraints weight = 1014.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2125  Z= 0.127
  Angle     :  0.558   6.864   2917  Z= 0.289
  Chirality :  0.040   0.127    368
  Planarity :  0.003   0.018    352
  Dihedral  :  5.601  42.620    303
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  7.35 %
    Allowed  : 27.94 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.53), residues: 277
  helix:  2.17 (0.35), residues: 213
  sheet:  None (None), residues: 0
  loop : -1.57 (0.87), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 278 
 TYR   0.009   0.001   TYR A 254 
 PHE   0.017   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.002   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 2124)
  covalent geometry    : angle       0.55774 ( 2915)
  SS BOND              : bond        0.00202 (    1)
  SS BOND              : angle       0.19799 (    2)
  hydrogen bonds       : bond        0.04019 (  162)
  hydrogen bonds       : angle       3.59440 (  480)

*********************** 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
  61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.078 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7709 (mtp)
REVERT: A  140 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7645 (tt)
REVERT: A  189 ILE cc_start: 0.8831 (mm) cc_final: 0.8483 (mm)
REVERT: A  338 TYR cc_start: 0.8671 (m-10) cc_final: 0.8234 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 56
  average time/residue: 0.0275
  time to fit residues: 2.1275
Evaluate side-chains
  57 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
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  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  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 24 optimal weight:    0.0670
   chunk 13 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.4980
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.147592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.127788 restraints weight = 4130.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.130739 restraints weight = 2221.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.132708 restraints weight = 1493.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133891 restraints weight = 1163.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133972 restraints weight = 994.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2296

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= 0.114
  Angle     :  0.526   6.240   2917  Z= 0.279
  Chirality :  0.040   0.127    368
  Planarity :  0.003   0.019    352
  Dihedral  :  5.499  42.768    303
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 27.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.53), residues: 277
  helix:  2.27 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.60 (0.88), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 278 
 TYR   0.011   0.001   TYR A 254 
 PHE   0.037   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.001   0.000   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 2124)
  covalent geometry    : angle       0.52592 ( 2915)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.26545 (    2)
  hydrogen bonds       : bond        0.03661 (  162)
  hydrogen bonds       : angle       3.54844 (  480)

********************** 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
  61 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7707 (tp)
REVERT: A  189 ILE cc_start: 0.8753 (mm) cc_final: 0.8431 (mm)
REVERT: A  338 TYR cc_start: 0.8649 (m-10) cc_final: 0.8270 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 56
  average time/residue: 0.0274
  time to fit residues: 2.1219
Evaluate side-chains
  56 residues out of total 256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 46
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  259 LEU
Chi-restraints excluded: chain A residue  280 ILE
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 12 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 5 optimal weight:    0.0870
   chunk 8 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.4758

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.147897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.128018 restraints weight = 4132.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.130721 restraints weight = 2229.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.132858 restraints weight = 1532.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.133997 restraints weight = 1192.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.134579 restraints weight = 1024.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2373

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= 0.115
  Angle     :  0.527   6.367   2917  Z= 0.279
  Chirality :  0.040   0.128    368
  Planarity :  0.003   0.018    352
  Dihedral  :  5.470  42.627    303
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 30.39 %
    Favored  : 64.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.53), residues: 277
  helix:  2.30 (0.35), residues: 214
  sheet:  None (None), residues: 0
  loop : -1.60 (0.88), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 278 
 TYR   0.011   0.001   TYR A 254 
 PHE   0.018   0.001   PHE A  89 
 TRP   0.008   0.001   TRP A 320 
 HIS   0.001   0.001   HIS A 299 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 2124)
  covalent geometry    : angle       0.52736 ( 2915)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.24469 (    2)
  hydrogen bonds       : bond        0.03674 (  162)
  hydrogen bonds       : angle       3.51408 (  480)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 661.11 seconds
wall clock time: 13 minutes 4.75 seconds (784.75 seconds total)