Starting phenix.real_space_refine
on Wed Sep 17 05:42:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o9s_70261/09_2025/9o9s_70261.map"
  }
  resolution = 3.57
  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=   0.003 sd=   0.962
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      18      5.16       5
     C    3440      2.51       5
     N     884      2.21       5
     O     980      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  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: 5322
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 442, 3438
          Classifications: {'peptide': 442}
          Link IDs: {'PTRANS': 25, 'TRANS': 416}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1862
          Classifications: {'peptide': 242}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 235}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Unusual residues: {'I2R': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.60, per 1000 atoms: 0.30
  Number of scatterers: 5322
  At special positions: 0
  Unit cell: (65.682, 98.154, 117.342, 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      18     16.00
     O     980      8.00
     N     884      7.00
     C    3440      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.46
  Conformation dependent library (CDL) restraints added in 206.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1262

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 4 sheets defined
      64.9% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 43
      Proline residue:  A  30  - end of helix
      Proline residue:  A  37  - end of helix
      removed outlier: 3.650A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 3.645A  pdb=" N   ILE A  51 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
      removed outlier: 3.552A  pdb=" N   LYS A  72 " --> pdb=" O   ARG A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 103
      removed outlier: 3.986A  pdb=" N   PHE A  81 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ALA A  82 " --> pdb=" O   TRP A  78 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   CYS A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   ASN A  87 " --> pdb=" O   CYS A  83 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU A  88 " --> pdb=" O   HIS A  84 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET A 103 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 153
    Processing helix  chain 'A' and resid 164 through 174
      Proline residue:  A 170  - end of helix
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 204 through 211
    Processing helix  chain 'A' and resid 212 through 219
      removed outlier: 3.684A  pdb=" N   VAL A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 4.729A  pdb=" N   ALA A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
      removed outlier: 3.847A  pdb=" N   THR A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      Proline residue:  A 281  - end of helix
      removed outlier: 4.434A  pdb=" N   ASP A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLY A 287 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 4.491A  pdb=" N   ASP A 306 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 307 through 323
    Processing helix  chain 'A' and resid 331 through 341
    Processing helix  chain 'A' and resid 350 through 352
      No H-bonds generated for 'chain 'A' and resid 350 through 352'
    Processing helix  chain 'A' and resid 353 through 360
      removed outlier: 3.562A  pdb=" N   ILE A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
    Processing helix  chain 'A' and resid 408 through 419
    Processing helix  chain 'A' and resid 426 through 434
    Processing helix  chain 'A' and resid 436 through 449
    Processing helix  chain 'A' and resid 457 through 474
    Processing helix  chain 'A' and resid 478 through 487
    Processing helix  chain 'B' and resid 43 through 62
      removed outlier: 3.869A  pdb=" N   ILE B  47 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 87
      removed outlier: 3.527A  pdb=" N   LEU B  87 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 137
      removed outlier: 3.695A  pdb=" N   ARG B 128 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 148
    Processing helix  chain 'B' and resid 161 through 170
      removed outlier: 3.573A  pdb=" N   LEU B 165 " --> pdb=" O   THR B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 181
    Processing helix  chain 'B' and resid 194 through 202
    Processing helix  chain 'B' and resid 204 through 214
      removed outlier: 3.605A  pdb=" N   ASN B 214 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 236
      removed outlier: 4.042A  pdb=" N   TRP B 235 " --> pdb=" O   LEU B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 247
    Processing helix  chain 'B' and resid 260 through 268
    Processing helix  chain 'B' and resid 270 through 281
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 160
      removed outlier: 6.775A  pdb=" N   GLY A 382 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   VAL A 232 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU A 384 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 160
    Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221
    Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 349

    314 hydrogen bonds defined for protein.
    921 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: 0.88

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 900
        1.27 -     1.40: 1349
        1.40 -     1.54: 3095
        1.54 -     1.67: 78
        1.67 -     1.81: 32
  Bond restraints: 5454
  Sorted by residual:
  bond pdb=" C19 I2R B 301 "
       pdb=" C22 I2R B 301 "
    ideal  model  delta    sigma   weight residual
    1.419  1.519 -0.100 2.00e-02 2.50e+03 2.50e+01
  bond pdb=" C12 I2R B 301 "
       pdb=" C7  I2R B 301 "
    ideal  model  delta    sigma   weight residual
    1.435  1.532 -0.097 2.00e-02 2.50e+03 2.36e+01
  bond pdb=" C5  I2R B 301 "
       pdb=" N3  I2R B 301 "
    ideal  model  delta    sigma   weight residual
    1.382  1.335  0.047 2.00e-02 2.50e+03 5.47e+00
  bond pdb=" C8  I2R B 301 "
       pdb=" N3  I2R B 301 "
    ideal  model  delta    sigma   weight residual
    1.359  1.315  0.044 2.00e-02 2.50e+03 4.78e+00
  bond pdb=" C9  I2R B 301 "
       pdb=" N3  I2R B 301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.449 -0.036 2.00e-02 2.50e+03 3.28e+00
  ... (remaining 5449 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 7308
        2.10 -     4.21: 82
        4.21 -     6.31: 12
        6.31 -     8.42: 7
        8.42 -    10.52: 2
  Bond angle restraints: 7411
  Sorted by residual:
  angle pdb=" CB  MET B  48 "
        pdb=" CG  MET B  48 "
        pdb=" SD  MET B  48 "
      ideal   model   delta    sigma   weight residual
     112.70  102.31   10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C   TRP B  94 "
        pdb=" N   SER B  95 "
        pdb=" CA  SER B  95 "
      ideal   model   delta    sigma   weight residual
     121.54  128.09   -6.55 1.91e+00 2.74e-01 1.18e+01
  angle pdb=" CB  LYS A  72 "
        pdb=" CG  LYS A  72 "
        pdb=" CD  LYS A  72 "
      ideal   model   delta    sigma   weight residual
     111.30  119.10   -7.80 2.30e+00 1.89e-01 1.15e+01
  angle pdb=" CA  LEU B 146 "
        pdb=" CB  LEU B 146 "
        pdb=" CG  LEU B 146 "
      ideal   model   delta    sigma   weight residual
     116.30  126.82  -10.52 3.50e+00 8.16e-02 9.04e+00
  angle pdb=" C   LEU B  87 "
        pdb=" N   VAL B  88 "
        pdb=" CA  VAL B  88 "
      ideal   model   delta    sigma   weight residual
     122.96  120.16    2.80 9.50e-01 1.11e+00 8.67e+00
  ... (remaining 7406 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.05: 2741
       18.05 -    36.11: 349
       36.11 -    54.16: 92
       54.16 -    72.21: 17
       72.21 -    90.27: 11
  Dihedral angle restraints: 3210
    sinusoidal: 1244
      harmonic: 1966
  Sorted by residual:
  dihedral pdb=" CA  MET B  48 "
           pdb=" C   MET B  48 "
           pdb=" N   LYS B  49 "
           pdb=" CA  LYS B  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.84   25.16     0      5.00e+00 4.00e-02 2.53e+01
  dihedral pdb=" CA  PHE B  43 "
           pdb=" C   PHE B  43 "
           pdb=" N   TRP B  44 "
           pdb=" CA  TRP B  44 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.02  -16.98     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  PHE A  66 "
           pdb=" C   PHE A  66 "
           pdb=" N   MET A  67 "
           pdb=" CA  MET A  67 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.45   16.55     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 3207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 546
       0.033 -    0.066: 185
       0.066 -    0.099: 55
       0.099 -    0.132: 24
       0.132 -    0.165: 3
  Chirality restraints: 813
  Sorted by residual:
  chirality pdb=" CA  MET B  48 "
            pdb=" N   MET B  48 "
            pdb=" C   MET B  48 "
            pdb=" CB  MET B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CA  ILE B  89 "
            pdb=" N   ILE B  89 "
            pdb=" C   ILE B  89 "
            pdb=" CB  ILE B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.92e-01
  chirality pdb=" CA  ILE A 181 "
            pdb=" N   ILE A 181 "
            pdb=" C   ILE A 181 "
            pdb=" CB  ILE A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 810 not shown)

  Planarity restraints: 950
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B  95 "   -0.013 2.00e-02 2.50e+03   2.55e-02 6.48e+00
        pdb=" C   SER B  95 "    0.044 2.00e-02 2.50e+03
        pdb=" O   SER B  95 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   LEU B  96 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B  48 "   -0.011 2.00e-02 2.50e+03   2.21e-02 4.87e+00
        pdb=" C   MET B  48 "    0.038 2.00e-02 2.50e+03
        pdb=" O   MET B  48 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LYS B  49 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A  29 "    0.032 5.00e-02 4.00e+02   4.86e-02 3.77e+00
        pdb=" N   PRO A  30 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A  30 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  30 "    0.027 5.00e-02 4.00e+02
  ... (remaining 947 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 775
        2.75 -     3.29: 5320
        3.29 -     3.83: 9015
        3.83 -     4.36: 10303
        4.36 -     4.90: 18104
  Nonbonded interactions: 43517
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 167 "
            pdb=" OH  TYR A 463 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" OD1 ASP B 222 "
            pdb=" N   MET B 226 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" O   GLU A 166 "
            pdb=" OH  TYR A 192 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   TYR A 212 "
            pdb=" OG1 THR A 215 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" N   GLU A 396 "
            pdb=" OE1 GLU A 396 "
     model   vdw
     2.287 3.120
  ... (remaining 43512 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.930
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.030
  Process input model:                     7.330
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
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      :  0.004   0.100   5454  Z= 0.190
  Angle     :  0.618  10.522   7411  Z= 0.308
  Chirality :  0.041   0.165    813
  Planarity :  0.005   0.049    950
  Dihedral  : 17.776  90.268   1948
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 25.65 %
    Favored  : 70.85 %
  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:  0.37 (0.33), residues: 678
  helix:  0.81 (0.27), residues: 406
  sheet:  0.16 (1.05), residues: 24
  loop : -0.57 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 143 
 TYR   0.010   0.001   TYR A 463 
 PHE   0.019   0.001   PHE A  66 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS A  26 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 5454)
  covalent geometry    : angle       0.61763 ( 7411)
  hydrogen bonds       : bond        0.14653 (  303)
  hydrogen bonds       : angle       6.86382 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   67 MET cc_start: 0.7137 (ttp) cc_final: 0.6513 (tpt)
REVERT: A   71 TYR cc_start: 0.7731 (t80) cc_final: 0.7491 (t80)
REVERT: B  212 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8269 (pt)
  outliers start: 19
  outliers final: 16
  residues processed: 81
  average time/residue: 0.0866
  time to fit residues: 9.0267
Evaluate side-chains
  79 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue  208 GLN
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  272 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A  91 GLN
A 208 GLN
A 404 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.141380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.116286 restraints weight = 6912.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.115004 restraints weight = 7486.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.115414 restraints weight = 7934.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.115701 restraints weight = 7269.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.115805 restraints weight = 6893.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5454  Z= 0.166
  Angle     :  0.591  11.376   7411  Z= 0.297
  Chirality :  0.041   0.158    813
  Planarity :  0.005   0.047    950
  Dihedral  :  8.452  59.667    766
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.69 %
    Favored  : 72.88 %
  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:  0.81 (0.33), residues: 678
  helix:  1.24 (0.26), residues: 410
  sheet:  0.36 (0.98), residues: 24
  loop : -0.57 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.017   0.001   TYR A 463 
 PHE   0.017   0.002   PHE A  66 
 TRP   0.008   0.001   TRP B  50 
 HIS   0.002   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5454)
  covalent geometry    : angle       0.59079 ( 7411)
  hydrogen bonds       : bond        0.04896 (  303)
  hydrogen bonds       : angle       5.03951 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   67 MET cc_start: 0.7048 (ttp) cc_final: 0.6583 (tpt)
REVERT: A   71 TYR cc_start: 0.7680 (t80) cc_final: 0.7443 (t80)
REVERT: B  212 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8344 (pt)
  outliers start: 24
  outliers final: 16
  residues processed: 90
  average time/residue: 0.0963
  time to fit residues: 10.9075
Evaluate side-chains
  75 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  408 THR
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  212 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 64 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 62 optimal weight:    0.4980
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.142743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.117579 restraints weight = 6858.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.116309 restraints weight = 7372.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.116696 restraints weight = 7854.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.117112 restraints weight = 7159.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.117277 restraints weight = 6795.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5454  Z= 0.136
  Angle     :  0.559   9.824   7411  Z= 0.280
  Chirality :  0.040   0.159    813
  Planarity :  0.005   0.045    950
  Dihedral  :  7.895  59.250    752
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 21.40 %
    Favored  : 73.62 %
  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:  1.02 (0.33), residues: 678
  helix:  1.44 (0.26), residues: 410
  sheet:  0.29 (0.95), residues: 24
  loop : -0.54 (0.40), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.012   0.001   TYR A 463 
 PHE   0.015   0.001   PHE A  66 
 TRP   0.008   0.001   TRP B  50 
 HIS   0.002   0.000   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5454)
  covalent geometry    : angle       0.55866 ( 7411)
  hydrogen bonds       : bond        0.04269 (  303)
  hydrogen bonds       : angle       4.72831 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 71
  time to evaluate  : 0.203 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8226 (OUTLIER) cc_final: 0.7538 (t80)
REVERT: A   67 MET cc_start: 0.7040 (ttp) cc_final: 0.6572 (tpt)
REVERT: A   71 TYR cc_start: 0.7607 (t80) cc_final: 0.7401 (t80)
REVERT: B  212 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8290 (pt)
  outliers start: 27
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0963
  time to fit residues: 10.9621
Evaluate side-chains
  81 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  212 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.139401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.114363 restraints weight = 6905.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.113531 restraints weight = 7595.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.113770 restraints weight = 7477.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.114023 restraints weight = 7015.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.114186 restraints weight = 6927.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5454  Z= 0.212
  Angle     :  0.611  11.846   7411  Z= 0.304
  Chirality :  0.043   0.151    813
  Planarity :  0.005   0.047    950
  Dihedral  :  7.897  59.568    752
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 22.14 %
    Favored  : 72.88 %
  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:  0.96 (0.32), residues: 678
  helix:  1.42 (0.26), residues: 405
  sheet:  0.19 (0.93), residues: 24
  loop : -0.56 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.012   0.001   TYR A  62 
 PHE   0.016   0.002   PHE A  69 
 TRP   0.008   0.001   TRP B  44 
 HIS   0.002   0.001   HIS B 164 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 5454)
  covalent geometry    : angle       0.61128 ( 7411)
  hydrogen bonds       : bond        0.04737 (  303)
  hydrogen bonds       : angle       4.73706 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.192 
Fit side-chains
REVERT: A   67 MET cc_start: 0.7078 (ttp) cc_final: 0.6606 (tpt)
  outliers start: 27
  outliers final: 22
  residues processed: 96
  average time/residue: 0.0941
  time to fit residues: 11.3773
Evaluate side-chains
  89 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue   89 ILE
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0980
   chunk 67 optimal weight:    8.9990
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0980
   chunk 58 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0070
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.2798

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.144220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.119281 restraints weight = 6933.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.118521 restraints weight = 7349.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.118807 restraints weight = 7805.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.119006 restraints weight = 6975.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.119208 restraints weight = 6757.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5454  Z= 0.117
  Angle     :  0.549   9.643   7411  Z= 0.274
  Chirality :  0.039   0.137    813
  Planarity :  0.005   0.047    950
  Dihedral  :  7.306  58.621    748
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 23.62 %
    Favored  : 72.51 %
  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:  1.10 (0.32), residues: 678
  helix:  1.53 (0.26), residues: 410
  sheet:  0.67 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.016   0.001   TYR A 463 
 PHE   0.016   0.001   PHE A  66 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5454)
  covalent geometry    : angle       0.54859 ( 7411)
  hydrogen bonds       : bond        0.03783 (  303)
  hydrogen bonds       : angle       4.44503 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8199 (OUTLIER) cc_final: 0.7441 (t80)
REVERT: A   71 TYR cc_start: 0.7555 (t80) cc_final: 0.7339 (t80)
  outliers start: 21
  outliers final: 16
  residues processed: 84
  average time/residue: 0.0921
  time to fit residues: 9.7013
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   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 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.117847 restraints weight = 6869.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.118735 restraints weight = 6078.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.119372 restraints weight = 5568.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.120214 restraints weight = 5200.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.120215 restraints weight = 4857.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5454  Z= 0.117
  Angle     :  0.548   9.643   7411  Z= 0.274
  Chirality :  0.039   0.137    813
  Planarity :  0.005   0.047    950
  Dihedral  :  7.314  58.621    748
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.17 %
    Favored  : 72.69 %
  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:  1.10 (0.32), residues: 678
  helix:  1.53 (0.26), residues: 410
  sheet:  0.67 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.016   0.001   TYR A 463 
 PHE   0.016   0.001   PHE A  66 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 5454)
  covalent geometry    : angle       0.54824 ( 7411)
  hydrogen bonds       : bond        0.03784 (  303)
  hydrogen bonds       : angle       4.44502 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7405 (t80)
REVERT: A   71 TYR cc_start: 0.7546 (t80) cc_final: 0.7338 (t80)
  outliers start: 17
  outliers final: 16
  residues processed: 74
  average time/residue: 0.1010
  time to fit residues: 9.3037
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.117826 restraints weight = 6918.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.118712 restraints weight = 6174.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.119144 restraints weight = 5594.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.120130 restraints weight = 5298.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.120499 restraints weight = 4998.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5454  Z= 0.117
  Angle     :  0.547   9.638   7411  Z= 0.274
  Chirality :  0.039   0.139    813
  Planarity :  0.005   0.047    950
  Dihedral  :  7.389  58.618    748
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.35 %
    Favored  : 72.51 %
  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:  1.10 (0.32), residues: 678
  helix:  1.53 (0.26), residues: 410
  sheet:  0.67 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 143 
 TYR   0.015   0.001   TYR A 463 
 PHE   0.016   0.001   PHE A  66 
 TRP   0.011   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 5454)
  covalent geometry    : angle       0.54715 ( 7411)
  hydrogen bonds       : bond        0.03788 (  303)
  hydrogen bonds       : angle       4.44487 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7407 (t80)
  outliers start: 17
  outliers final: 16
  residues processed: 74
  average time/residue: 0.1003
  time to fit residues: 9.2801
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118038 restraints weight = 6749.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118038 restraints weight = 6014.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118038 restraints weight = 6014.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118038 restraints weight = 6014.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.118038 restraints weight = 6014.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5454  Z= 0.120
  Angle     :  0.545   9.623   7411  Z= 0.273
  Chirality :  0.039   0.145    813
  Planarity :  0.005   0.046    950
  Dihedral  :  7.574  58.610    748
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.17 %
    Favored  : 72.69 %
  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:  1.10 (0.32), residues: 678
  helix:  1.53 (0.26), residues: 410
  sheet:  0.68 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.014   0.001   TYR A 463 
 PHE   0.015   0.001   PHE A  66 
 TRP   0.010   0.001   TRP B  50 
 HIS   0.003   0.001   HIS A 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 5454)
  covalent geometry    : angle       0.54496 ( 7411)
  hydrogen bonds       : bond        0.03800 (  303)
  hydrogen bonds       : angle       4.44444 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7429 (t80)
  outliers start: 17
  outliers final: 16
  residues processed: 74
  average time/residue: 0.1050
  time to fit residues: 9.7970
Evaluate side-chains
  80 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0270
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0870
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.144547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.119169 restraints weight = 6829.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.119765 restraints weight = 6090.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.119765 restraints weight = 5637.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.119765 restraints weight = 5637.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.119765 restraints weight = 5637.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5454  Z= 0.134
  Angle     :  0.586  10.415   7411  Z= 0.288
  Chirality :  0.040   0.157    813
  Planarity :  0.005   0.046    950
  Dihedral  :  7.260  58.422    748
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 23.43 %
    Favored  : 72.69 %
  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:  1.13 (0.32), residues: 678
  helix:  1.56 (0.26), residues: 410
  sheet:  0.70 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 143 
 TYR   0.015   0.001   TYR A 463 
 PHE   0.015   0.001   PHE A  66 
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5454)
  covalent geometry    : angle       0.58554 ( 7411)
  hydrogen bonds       : bond        0.03768 (  303)
  hydrogen bonds       : angle       4.42262 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7370 (t80)
  outliers start: 21
  outliers final: 18
  residues processed: 77
  average time/residue: 0.0974
  time to fit residues: 9.4493
Evaluate side-chains
  82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0570
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.119183 restraints weight = 6918.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.118379 restraints weight = 7134.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.118537 restraints weight = 7492.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.118825 restraints weight = 6881.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.118934 restraints weight = 6728.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5454  Z= 0.134
  Angle     :  0.585  10.415   7411  Z= 0.288
  Chirality :  0.040   0.157    813
  Planarity :  0.005   0.046    950
  Dihedral  :  7.260  58.422    748
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.62 %
    Favored  : 72.88 %
  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:  1.13 (0.32), residues: 678
  helix:  1.56 (0.26), residues: 410
  sheet:  0.70 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 143 
 TYR   0.015   0.001   TYR A 463 
 PHE   0.015   0.001   PHE A  66 
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5454)
  covalent geometry    : angle       0.58547 ( 7411)
  hydrogen bonds       : bond        0.03768 (  303)
  hydrogen bonds       : angle       4.42262 (  921)

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   62 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7440 (t80)
  outliers start: 19
  outliers final: 18
  residues processed: 75
  average time/residue: 0.1038
  time to fit residues: 9.7580
Evaluate side-chains
  82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 TRP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   62 TYR
Chi-restraints excluded: chain A residue   63 SER
Chi-restraints excluded: chain A residue   83 CYS
Chi-restraints excluded: chain A residue  368 VAL
Chi-restraints excluded: chain A residue  380 PHE
Chi-restraints excluded: chain A residue  429 TYR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   60 MET
Chi-restraints excluded: chain B residue   62 ARG
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   88 VAL
Chi-restraints excluded: chain B residue  168 TYR
Chi-restraints excluded: chain B residue  180 LYS
Chi-restraints excluded: chain B residue  193 TYR
Chi-restraints excluded: chain B residue  211 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0870
   chunk 4 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.143826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.119462 restraints weight = 6835.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.118545 restraints weight = 7087.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.118838 restraints weight = 7433.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.119166 restraints weight = 6864.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.119290 restraints weight = 6557.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5454  Z= 0.134
  Angle     :  0.585  10.415   7411  Z= 0.288
  Chirality :  0.040   0.157    813
  Planarity :  0.005   0.046    950
  Dihedral  :  7.260  58.422    748
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.80 %
    Favored  : 72.69 %
  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:  1.13 (0.32), residues: 678
  helix:  1.56 (0.26), residues: 410
  sheet:  0.70 (0.99), residues: 24
  loop : -0.60 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 143 
 TYR   0.015   0.001   TYR A 463 
 PHE   0.015   0.001   PHE A  66 
 TRP   0.010   0.001   TRP B  50 
 HIS   0.002   0.001   HIS B 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 5454)
  covalent geometry    : angle       0.58547 ( 7411)
  hydrogen bonds       : bond        0.03768 (  303)
  hydrogen bonds       : angle       4.42262 (  921)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1084.00 seconds
wall clock time: 19 minutes 26.38 seconds (1166.38 seconds total)