Starting phenix.real_space_refine
on Wed Sep 17 06:52:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dax_46701/09_2025/9dax_46701.map"
  }
  resolution = 3.3
  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=   0.050
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: 6
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     Mg      1      5.21       5
     S      26      5.16       5
     C    4037      2.51       5
     N    1091      2.21       5
     O    1240      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 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: 6401
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3468
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
      Conformer: "B"
        Number of residues, atoms: 451, 3460
          Classifications: {'peptide': 451}
          Link IDs: {'PTRANS': 26, 'TRANS': 424}
          bond proxies already assigned to first conformer: 3546
    Chain: "B"
      Number of atoms: 2920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2920
          Classifications: {'peptide': 374}
          Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 355}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' CA': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Unusual residues: {' CA': 2, ' MG': 1}
          Classifications: {'undetermined': 3, 'water': 6}
          Link IDs: {None: 8}
  Time building chain proxies: 2.39, per 1000 atoms: 0.37
  Number of scatterers: 6401
  At special positions: 0
  Unit cell: (65.36, 104.06, 84.28, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      6     19.99
     S      26     16.00
     Mg      1     11.99
     O    1240      8.00
     N    1091      7.00
     C    4037      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  56 " - pdb=" SG  CYS A  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 107 " - pdb=" SG  CYS A 130 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 146 " - pdb=" SG  CYS A 167 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 184 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 232 " - pdb=" SG  CYS B 273 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 374 " - pdb=" SG  CYS B 386 " 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: 0.44
  Conformation dependent library (CDL) restraints added in 450.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 14 sheets defined
      13.1% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 151 through 159
    Processing helix  chain 'A' and resid 187 through 192
    Processing helix  chain 'A' and resid 200 through 206
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 3.524A  pdb=" N   PHE A 231 " --> pdb=" O   PRO A 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 80
    Processing helix  chain 'B' and resid 121 through 123
      No H-bonds generated for 'chain 'B' and resid 121 through 123'
    Processing helix  chain 'B' and resid 124 through 129
      removed outlier: 3.855A  pdb=" N   LEU B 128 " --> pdb=" O   MET B 124 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   TRP B 129 " --> pdb=" O   LYS B 125 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 124 through 129'
    Processing helix  chain 'B' and resid 133 through 144
      removed outlier: 4.032A  pdb=" N   LYS B 144 " --> pdb=" O   THR B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 207
      removed outlier: 3.983A  pdb=" N   ASN B 204 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 232
      removed outlier: 3.811A  pdb=" N   ALA B 225 " --> pdb=" O   GLY B 221 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   CYS B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 237
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.590A  pdb=" N   THR B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.638A  pdb=" N   TYR B 318 " --> pdb=" O   VAL B 314 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 353
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 63
      removed outlier: 3.653A  pdb=" N   ILE A 436 " --> pdb=" O   ARG A 422 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 420 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27
    Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79
      removed outlier: 3.537A  pdb=" N   GLU A  75 " --> pdb=" O   THR A  86 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100
    Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133
    Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 239 through 242
    Processing sheet with id=AA8, first strand: chain 'A' and resid 306 through 310
    Processing sheet with id=AA9, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AB1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 3.618A  pdb=" N   ALA A 361 " --> pdb=" O   ALA A 375 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   ASP A 373 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLN A 405 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 394 through 395
    Processing sheet with id=AB3, first strand: chain 'B' and resid 63 through 65
      removed outlier: 6.368A  pdb=" N   ARG B  87 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ILE B  88 " --> pdb=" O   ILE B 426 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 97 through 102
    Processing sheet with id=AB5, first strand: chain 'B' and resid 194 through 197
      removed outlier: 4.164A  pdb=" N   LEU B 196 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   ILE B 151 " --> pdb=" O   LEU B 196 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASP B 113 " --> pdb=" O   SER B 243 " (cutoff:3.500A)

    188 hydrogen bonds defined for protein.
    476 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: 0.97

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        0.90 -     1.09: 2
        1.09 -     1.28: 1084
        1.28 -     1.46: 2576
        1.46 -     1.65: 2835
        1.65 -     1.84: 39
  Bond restraints: 6536
  Sorted by residual:
  bond pdb=" CB  PRO A 410 "
       pdb=" CG  PRO A 410 "
    ideal  model  delta    sigma   weight residual
    1.492  0.899  0.593 5.00e-02 4.00e+02 1.41e+02
  bond pdb=" C   LYS B 298 "
       pdb=" O   LYS B 298 "
    ideal  model  delta    sigma   weight residual
    1.235  1.086  0.149 1.26e-02 6.30e+03 1.40e+02
  bond pdb=" N   LYS B 298 "
       pdb=" CA  LYS B 298 "
    ideal  model  delta    sigma   weight residual
    1.457  1.325  0.132 1.29e-02 6.01e+03 1.05e+02
  bond pdb=" CG  PRO A 410 "
       pdb=" CD  PRO A 410 "
    ideal  model  delta    sigma   weight residual
    1.503  1.234  0.269 3.40e-02 8.65e+02 6.26e+01
  bond pdb=" N   LEU B 299 "
       pdb=" CA  LEU B 299 "
    ideal  model  delta    sigma   weight residual
    1.456  1.544 -0.088 1.32e-02 5.74e+03 4.43e+01
  ... (remaining 6531 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.62: 8872
       11.62 -    23.23: 6
       23.23 -    34.85: 3
       34.85 -    46.46: 0
       46.46 -    58.08: 1
  Bond angle restraints: 8882
  Sorted by residual:
  angle pdb=" N   PRO A 410 "
        pdb=" CD  PRO A 410 "
        pdb=" CG  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     103.20   75.64   27.56 1.50e+00 4.44e-01 3.38e+02
  angle pdb=" CB  PRO A 410 "
        pdb=" CG  PRO A 410 "
        pdb=" CD  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     106.10  164.18  -58.08 3.20e+00 9.77e-02 3.29e+02
  angle pdb=" CA  PRO A 410 "
        pdb=" CB  PRO A 410 "
        pdb=" CG  PRO A 410 "
      ideal   model   delta    sigma   weight residual
     104.50   70.31   34.19 1.90e+00 2.77e-01 3.24e+02
  angle pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
        pdb=" C   GLU B 297 "
      ideal   model   delta    sigma   weight residual
     110.80   86.71   24.09 2.13e+00 2.20e-01 1.28e+02
  angle pdb=" N   LEU B 299 "
        pdb=" CA  LEU B 299 "
        pdb=" CB  LEU B 299 "
      ideal   model   delta    sigma   weight residual
     110.53  123.48  -12.95 1.47e+00 4.63e-01 7.76e+01
  ... (remaining 8877 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.35: 3382
       19.35 -    38.69: 398
       38.69 -    58.04: 93
       58.04 -    77.38: 17
       77.38 -    96.73: 9
  Dihedral angle restraints: 3899
    sinusoidal: 1539
      harmonic: 2360
  Sorted by residual:
  dihedral pdb=" N   LEU B 299 "
           pdb=" C   LEU B 299 "
           pdb=" CA  LEU B 299 "
           pdb=" CB  LEU B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  155.80  -33.00     0      2.50e+00 1.60e-01 1.74e+02
  dihedral pdb=" C   LEU B 299 "
           pdb=" N   LEU B 299 "
           pdb=" CA  LEU B 299 "
           pdb=" CB  LEU B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -152.97   30.37     0      2.50e+00 1.60e-01 1.48e+02
  dihedral pdb=" CB  CYS A 107 "
           pdb=" SG  CYS A 107 "
           pdb=" SG  CYS A 130 "
           pdb=" CB  CYS A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.66   81.34     1      1.00e+01 1.00e-02 8.15e+01
  ... (remaining 3896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.283: 968
       0.283 -    0.565: 2
       0.565 -    0.848: 0
       0.848 -    1.131: 0
       1.131 -    1.414: 1
  Chirality restraints: 971
  Sorted by residual:
  chirality pdb=" CA  LEU B 299 "
            pdb=" N   LEU B 299 "
            pdb=" C   LEU B 299 "
            pdb=" CB  LEU B 299 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 5.00e+01
  chirality pdb=" CA  MET B 295 "
            pdb=" N   MET B 295 "
            pdb=" C   MET B 295 "
            pdb=" CB  MET B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.96e+00
  chirality pdb=" CA  GLU B 297 "
            pdb=" N   GLU B 297 "
            pdb=" C   GLU B 297 "
            pdb=" CB  GLU B 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.97   -0.46 2.00e-01 2.50e+01 5.35e+00
  ... (remaining 968 not shown)

  Planarity restraints: 1170
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 110 "    0.071 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO B 111 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO B 111 "    0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO B 111 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  56 "   -0.054 5.00e-02 4.00e+02   8.24e-02 1.09e+01
        pdb=" N   PRO A  57 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A  57 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A  57 "   -0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 294 "    0.017 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   LEU B 294 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   LEU B 294 "    0.020 2.00e-02 2.50e+03
        pdb=" N   MET B 295 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1167 not shown)

  Histogram of nonbonded interaction distances:
        0.91 -     1.71: 3
        1.71 -     2.51: 105
        2.51 -     3.30: 7238
        3.30 -     4.10: 15863
        4.10 -     4.90: 29247
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 52456
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU B 299 "
            pdb=" CG2 ILE B 304 "
     model   vdw
     0.912 3.880
  nonbonded pdb=" CD1 LEU B 299 "
            pdb=" CB  ILE B 304 "
     model   vdw
     1.453 3.890
  nonbonded pdb=" CG  LEU B 299 "
            pdb=" CG2 ILE B 304 "
     model   vdw
     1.571 3.890
  nonbonded pdb=" CB  ILE B 226 "
            pdb=" CE  MET B 295 "
     model   vdw
     1.840 3.890
  nonbonded pdb=" CG2 ILE B 226 "
            pdb=" CE  MET B 295 "
     model   vdw
     1.863 3.880
  ... (remaining 52451 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=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.750
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.340
  Find NCS groups from input model:        0.030
  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:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
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      :  0.010   0.593   6542  Z= 0.373
  Angle     :  1.227  58.077   8894  Z= 0.622
  Chirality :  0.069   1.414    971
  Planarity :  0.007   0.103   1170
  Dihedral  : 17.643  96.728   2381
  Min Nonbonded Distance : 0.912

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  4.51 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 24.89 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.40 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.15 (0.28), residues: 822
  helix: -1.81 (0.49), residues: 88
  sheet: -1.23 (0.31), residues: 252
  loop : -1.45 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 261 
 TYR   0.017   0.001   TYR A 288 
 PHE   0.019   0.002   PHE B 414 
 TRP   0.032   0.002   TRP A 260 
 HIS   0.006   0.001   HIS B 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00965 ( 6536)
  covalent geometry    : angle       1.22694 ( 8882)
  SS BOND              : bond        0.00502 (    6)
  SS BOND              : angle       1.24819 (   12)
  hydrogen bonds       : bond        0.26885 (  188)
  hydrogen bonds       : angle      10.66624 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0814
  time to fit residues: 6.5796
Evaluate side-chains
  55 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  298 LYS
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  304 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
A 284 GLN
A 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.240707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4587 r_free = 0.4587 target = 0.213513 restraints weight = 8158.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4625 rms_B_bonded: 2.11
r_work: 0.4345 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4372 r_free = 0.4372    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4373 r_free = 0.4373    target_work(ls_wunit_k1) = 0.183         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087   6542  Z= 0.157
  Angle     :  0.747  17.104   8894  Z= 0.383
  Chirality :  0.047   0.206    971
  Planarity :  0.006   0.069   1170
  Dihedral  :  5.325  36.575    915
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.37 %
    Allowed  :  5.48 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.58 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -1.78 (0.28), residues: 822
  helix: -1.19 (0.50), residues: 80
  sheet: -1.17 (0.31), residues: 258
  loop : -1.15 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  90 
 TYR   0.021   0.002   TYR A 288 
 PHE   0.017   0.002   PHE A 356 
 TRP   0.023   0.002   TRP A 260 
 HIS   0.006   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6536)
  covalent geometry    : angle       0.74548 ( 8882)
  SS BOND              : bond        0.00388 (    6)
  SS BOND              : angle       1.34266 (   12)
  hydrogen bonds       : bond        0.03892 (  188)
  hydrogen bonds       : angle       7.49564 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 61
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 PRO cc_start: 0.7431 (OUTLIER) cc_final: 0.7022 (Cg_exo)
REVERT: B  181 LYS cc_start: 0.7564 (mtpp) cc_final: 0.6910 (tppt)
REVERT: B  321 TYR cc_start: 0.3246 (OUTLIER) cc_final: 0.2050 (t80)
REVERT: B  342 GLN cc_start: 0.6820 (tp40) cc_final: 0.6583 (mm110)
  outliers start: 18
  outliers final: 5
  residues processed: 77
  average time/residue: 0.0781
  time to fit residues: 8.3376
Evaluate side-chains
  60 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  321 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
A 333 GLN
A 443 ASN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4747 r_free = 0.4747 target = 0.226999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.209352 restraints weight = 10098.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.4610 rms_B_bonded: 0.96
r_work: 0.4370 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work (final): 0.4370
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4394 r_free = 0.4394    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4394 r_free = 0.4394    target_work(ls_wunit_k1) = 0.186         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6565
moved from start:          0.2326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106   6542  Z= 0.284
  Angle     :  0.909  15.675   8894  Z= 0.466
  Chirality :  0.052   0.202    971
  Planarity :  0.007   0.073   1170
  Dihedral  :  5.660  28.258    904
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.06 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 21.29 %
    Favored  : 74.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.36 (0.27), residues: 822
  helix: -1.66 (0.45), residues: 92
  sheet: -1.32 (0.31), residues: 259
  loop : -1.68 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 335 
 TYR   0.028   0.003   TYR A 190 
 PHE   0.022   0.003   PHE A 356 
 TRP   0.029   0.003   TRP A 260 
 HIS   0.006   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00668 ( 6536)
  covalent geometry    : angle       0.90632 ( 8882)
  SS BOND              : bond        0.01290 (    6)
  SS BOND              : angle       1.94459 (   12)
  hydrogen bonds       : bond        0.04769 (  188)
  hydrogen bonds       : angle       7.68742 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 PRO cc_start: 0.7482 (OUTLIER) cc_final: 0.7115 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4652 (OUTLIER) cc_final: 0.4112 (tt)
REVERT: B  181 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7119 (tppt)
REVERT: B  193 VAL cc_start: 0.6629 (OUTLIER) cc_final: 0.6425 (m)
REVERT: B  209 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6972 (pttm)
REVERT: B  321 TYR cc_start: 0.3719 (OUTLIER) cc_final: 0.2464 (t80)
REVERT: B  413 SER cc_start: 0.7163 (OUTLIER) cc_final: 0.6943 (t)
  outliers start: 28
  outliers final: 13
  residues processed: 94
  average time/residue: 0.0915
  time to fit residues: 11.3628
Evaluate side-chains
  80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 61
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  203 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue   88 ILE
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  413 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 13 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4780 r_free = 0.4780 target = 0.230329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 89)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.200514 restraints weight = 8519.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4499 rms_B_bonded: 2.09
r_work: 0.4266 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4271
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4271 r_free = 0.4271    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4271 r_free = 0.4271    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4271
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   6542  Z= 0.186
  Angle     :  0.793  16.070   8894  Z= 0.402
  Chirality :  0.050   0.368    971
  Planarity :  0.006   0.079   1170
  Dihedral  :  5.276  26.934    904
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  6.21 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.73 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.20 (0.27), residues: 822
  helix: -1.35 (0.48), residues: 91
  sheet: -1.20 (0.32), residues: 245
  loop : -1.63 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 261 
 TYR   0.023   0.002   TYR A 380 
 PHE   0.019   0.002   PHE A  19 
 TRP   0.023   0.002   TRP A 260 
 HIS   0.004   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 6536)
  covalent geometry    : angle       0.79184 ( 8882)
  SS BOND              : bond        0.00497 (    6)
  SS BOND              : angle       1.53710 (   12)
  hydrogen bonds       : bond        0.03726 (  188)
  hydrogen bonds       : angle       7.25059 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: A  191 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.6648 (m-80)
REVERT: A  204 PHE cc_start: 0.3684 (OUTLIER) cc_final: 0.3156 (m-10)
REVERT: A  410 PRO cc_start: 0.7456 (OUTLIER) cc_final: 0.7050 (Cg_exo)
REVERT: B  181 LYS cc_start: 0.7752 (mtpp) cc_final: 0.7036 (tppt)
REVERT: B  209 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7187 (pttm)
REVERT: B  258 LEU cc_start: 0.6288 (mp) cc_final: 0.5731 (mt)
REVERT: B  321 TYR cc_start: 0.4023 (OUTLIER) cc_final: 0.2498 (t80)
  outliers start: 27
  outliers final: 11
  residues processed: 93
  average time/residue: 0.0914
  time to fit residues: 11.2466
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain B residue   80 VAL
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.227982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.197376 restraints weight = 8567.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.4475 rms_B_bonded: 2.20
r_work: 0.4175 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.4175
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4190
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4190 r_free = 0.4190    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4190
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   6542  Z= 0.197
  Angle     :  0.808  16.038   8894  Z= 0.404
  Chirality :  0.049   0.269    971
  Planarity :  0.006   0.080   1170
  Dihedral  :  5.273  24.689    904
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.19 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 21.73 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.27 (0.27), residues: 822
  helix: -1.51 (0.48), residues: 91
  sheet: -1.18 (0.32), residues: 243
  loop : -1.70 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 165 
 TYR   0.023   0.002   TYR A 190 
 PHE   0.019   0.002   PHE A  19 
 TRP   0.022   0.002   TRP A 260 
 HIS   0.004   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 6536)
  covalent geometry    : angle       0.80594 ( 8882)
  SS BOND              : bond        0.00537 (    6)
  SS BOND              : angle       1.59180 (   12)
  hydrogen bonds       : bond        0.03728 (  188)
  hydrogen bonds       : angle       7.07026 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 66
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  191 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6685 (m-80)
REVERT: A  204 PHE cc_start: 0.3664 (OUTLIER) cc_final: 0.3118 (m-10)
REVERT: A  410 PRO cc_start: 0.7331 (OUTLIER) cc_final: 0.6910 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4567 (OUTLIER) cc_final: 0.4003 (tt)
REVERT: B  181 LYS cc_start: 0.7749 (mtpp) cc_final: 0.7030 (tppt)
REVERT: B  209 LYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7299 (pttm)
REVERT: B  215 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7814 (p0)
REVERT: B  321 TYR cc_start: 0.4382 (OUTLIER) cc_final: 0.2661 (t80)
  outliers start: 33
  outliers final: 16
  residues processed: 96
  average time/residue: 0.0970
  time to fit residues: 12.1746
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 215 HIS
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 274 HIS
B 428 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.226723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.208825 restraints weight = 12181.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.4607 rms_B_bonded: 1.41
r_work: 0.4252 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4286
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4286 r_free = 0.4286    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4286 r_free = 0.4286    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4286
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6659
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.096   6542  Z= 0.200
  Angle     :  0.798  16.063   8894  Z= 0.401
  Chirality :  0.050   0.328    971
  Planarity :  0.006   0.080   1170
  Dihedral  :  5.339  26.986    904
  Min Nonbonded Distance : 1.863

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.94 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 23.02 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.29 (0.28), residues: 822
  helix: -1.48 (0.48), residues: 91
  sheet: -1.17 (0.33), residues: 243
  loop : -1.74 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  87 
 TYR   0.022   0.002   TYR A 190 
 PHE   0.019   0.002   PHE A  19 
 TRP   0.016   0.002   TRP A 260 
 HIS   0.004   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6536)
  covalent geometry    : angle       0.79678 ( 8882)
  SS BOND              : bond        0.00559 (    6)
  SS BOND              : angle       1.59435 (   12)
  hydrogen bonds       : bond        0.03685 (  188)
  hydrogen bonds       : angle       7.04400 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  191 PHE cc_start: 0.7044 (OUTLIER) cc_final: 0.6776 (m-80)
REVERT: A  204 PHE cc_start: 0.4070 (OUTLIER) cc_final: 0.3448 (m-10)
REVERT: A  410 PRO cc_start: 0.7495 (OUTLIER) cc_final: 0.7089 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4644 (tt)
REVERT: B  209 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7061 (pttm)
REVERT: B  215 ASN cc_start: 0.8180 (OUTLIER) cc_final: 0.7904 (p0)
REVERT: B  321 TYR cc_start: 0.4329 (OUTLIER) cc_final: 0.2776 (t80)
  outliers start: 33
  outliers final: 19
  residues processed: 88
  average time/residue: 0.0822
  time to fit residues: 9.8576
Evaluate side-chains
  83 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 57
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue   83 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  379 VAL
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 81 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 21 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
B 106 GLN
B 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.229473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.198069 restraints weight = 8168.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4468 rms_B_bonded: 2.02
r_work: 0.4243 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.174         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   6542  Z= 0.155
  Angle     :  0.732  16.129   8894  Z= 0.368
  Chirality :  0.047   0.274    971
  Planarity :  0.006   0.072   1170
  Dihedral  :  5.079  27.559    904
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.70 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 23.74 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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 (0.28), residues: 822
  helix: -1.44 (0.48), residues: 92
  sheet: -1.17 (0.32), residues: 245
  loop : -1.66 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  87 
 TYR   0.020   0.002   TYR A 380 
 PHE   0.018   0.002   PHE A 356 
 TRP   0.015   0.002   TRP A 260 
 HIS   0.003   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6536)
  covalent geometry    : angle       0.73075 ( 8882)
  SS BOND              : bond        0.00488 (    6)
  SS BOND              : angle       1.37902 (   12)
  hydrogen bonds       : bond        0.03298 (  188)
  hydrogen bonds       : angle       6.78144 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 58
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  204 PHE cc_start: 0.3574 (OUTLIER) cc_final: 0.2959 (m-10)
REVERT: A  410 PRO cc_start: 0.7465 (OUTLIER) cc_final: 0.7053 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4672 (OUTLIER) cc_final: 0.4147 (tt)
REVERT: B  181 LYS cc_start: 0.7608 (mtpp) cc_final: 0.7041 (tppt)
REVERT: B  209 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7344 (pttm)
REVERT: B  215 ASN cc_start: 0.7965 (OUTLIER) cc_final: 0.7720 (p0)
REVERT: B  321 TYR cc_start: 0.4077 (OUTLIER) cc_final: 0.2580 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 82
  average time/residue: 0.0850
  time to fit residues: 9.4660
Evaluate side-chains
  80 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 57
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  209 LYS
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  261 ARG
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  319 GLN
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0670
   chunk 40 optimal weight:    0.0570
   chunk 48 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0770
   overall best weight:    0.2394

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

Flipped N/Q/H residues before XYZ refinement:
A  82 GLN
A 219 GLN
A 333 GLN
** B 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.233563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.216759 restraints weight = 12071.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.4675 rms_B_bonded: 1.23
r_work: 0.4366 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.4366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4400 r_free = 0.4400    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4400 r_free = 0.4400    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6449
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091   6542  Z= 0.119
  Angle     :  0.685  16.185   8894  Z= 0.347
  Chirality :  0.045   0.158    971
  Planarity :  0.005   0.065   1170
  Dihedral  :  4.828  27.506    904
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.75 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.61 %
    Favored  : 71.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.06 (0.28), residues: 822
  helix: -1.26 (0.47), residues: 99
  sheet: -1.10 (0.33), residues: 246
  loop : -1.54 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  87 
 TYR   0.017   0.002   TYR A 380 
 PHE   0.016   0.001   PHE A 356 
 TRP   0.011   0.001   TRP A 260 
 HIS   0.002   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6536)
  covalent geometry    : angle       0.68412 ( 8882)
  SS BOND              : bond        0.00448 (    6)
  SS BOND              : angle       1.17267 (   12)
  hydrogen bonds       : bond        0.02868 (  188)
  hydrogen bonds       : angle       6.51901 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.4093 (OUTLIER) cc_final: 0.3517 (m-10)
REVERT: A  410 PRO cc_start: 0.7543 (OUTLIER) cc_final: 0.7143 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.5220 (OUTLIER) cc_final: 0.4670 (tt)
  outliers start: 18
  outliers final: 12
  residues processed: 74
  average time/residue: 0.0901
  time to fit residues: 8.9894
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  333 GLN
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  269 ASN
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  321 TYR
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 59 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.228238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.209607 restraints weight = 10087.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.4615 rms_B_bonded: 1.02
r_work: 0.4318 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4347 r_free = 0.4347    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4347 r_free = 0.4347    target_work(ls_wunit_k1) = 0.181         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095   6542  Z= 0.183
  Angle     :  0.766  16.100   8894  Z= 0.387
  Chirality :  0.047   0.212    971
  Planarity :  0.006   0.062   1170
  Dihedral  :  5.033  26.160    904
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 13.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.46 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.90 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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 (0.28), residues: 822
  helix: -1.41 (0.47), residues: 99
  sheet: -1.14 (0.33), residues: 251
  loop : -1.62 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 261 
 TYR   0.021   0.002   TYR A 380 
 PHE   0.019   0.002   PHE A 356 
 TRP   0.015   0.002   TRP A 260 
 HIS   0.003   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 6536)
  covalent geometry    : angle       0.76493 ( 8882)
  SS BOND              : bond        0.00540 (    6)
  SS BOND              : angle       1.48103 (   12)
  hydrogen bonds       : bond        0.03363 (  188)
  hydrogen bonds       : angle       6.74242 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  204 PHE cc_start: 0.4033 (OUTLIER) cc_final: 0.3450 (m-10)
REVERT: A  410 PRO cc_start: 0.7546 (OUTLIER) cc_final: 0.7141 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.5163 (OUTLIER) cc_final: 0.4652 (tt)
REVERT: B  215 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7790 (p0)
  outliers start: 19
  outliers final: 12
  residues processed: 76
  average time/residue: 0.0875
  time to fit residues: 8.9703
Evaluate side-chains
  74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  319 GLN
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 80 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0050
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.3980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A 333 GLN
B 269 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4775 r_free = 0.4775 target = 0.229981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.197939 restraints weight = 13164.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.4470 rms_B_bonded: 2.88
r_work (final): 0.4470
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4469
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4469 r_free = 0.4469    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4469 r_free = 0.4469    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4469
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6427
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   6542  Z= 0.154
  Angle     :  0.738  16.140   8894  Z= 0.373
  Chirality :  0.046   0.150    971
  Planarity :  0.005   0.059   1170
  Dihedral  :  4.954  26.052    904
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 13.41
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.72 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 25.90 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.11 (0.28), residues: 822
  helix: -1.30 (0.48), residues: 99
  sheet: -1.20 (0.32), residues: 257
  loop : -1.52 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 261 
 TYR   0.020   0.002   TYR A 288 
 PHE   0.019   0.002   PHE A 356 
 TRP   0.013   0.002   TRP A 260 
 HIS   0.002   0.001   HIS A 291 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6536)
  covalent geometry    : angle       0.73646 ( 8882)
  SS BOND              : bond        0.00499 (    6)
  SS BOND              : angle       1.35108 (   12)
  hydrogen bonds       : bond        0.03121 (  188)
  hydrogen bonds       : angle       6.66246 (  476)

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

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

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1644 Ramachandran restraints generated.
    822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 GLU cc_start: 0.5447 (mp0) cc_final: 0.5159 (mp0)
REVERT: A  204 PHE cc_start: 0.3903 (OUTLIER) cc_final: 0.3340 (m-10)
REVERT: A  410 PRO cc_start: 0.7483 (OUTLIER) cc_final: 0.7102 (Cg_exo)
REVERT: A  427 ILE cc_start: 0.4706 (OUTLIER) cc_final: 0.4214 (tt)
REVERT: B  215 ASN cc_start: 0.7780 (OUTLIER) cc_final: 0.7501 (p0)
  outliers start: 18
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0871
  time to fit residues: 8.8570
Evaluate side-chains
  72 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 55
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 SER
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  130 CYS
Chi-restraints excluded: chain A residue  204 PHE
Chi-restraints excluded: chain A residue  410 PRO
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  215 ASN
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  280 HIS
Chi-restraints excluded: chain B residue  424 SER
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  430 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0770
   chunk 34 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.4766 r_free = 0.4766 target = 0.228808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.210947 restraints weight = 12036.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.4626 rms_B_bonded: 1.37
r_work: 0.4283 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.4283
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4314 r_free = 0.4314    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4314 r_free = 0.4314    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.094   6542  Z= 0.164
  Angle     :  0.752  16.123   8894  Z= 0.379
  Chirality :  0.046   0.149    971
  Planarity :  0.005   0.057   1170
  Dihedral  :  4.981  25.165    904
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.97 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.04 %
    Favored  : 71.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.82 %
    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: -2.08 (0.28), residues: 822
  helix: -1.31 (0.49), residues: 100
  sheet: -1.21 (0.32), residues: 257
  loop : -1.46 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 261 
 TYR   0.028   0.002   TYR A 288 
 PHE   0.019   0.002   PHE A 356 
 TRP   0.013   0.002   TRP A 260 
 HIS   0.002   0.001   HIS B 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6536)
  covalent geometry    : angle       0.75092 ( 8882)
  SS BOND              : bond        0.00510 (    6)
  SS BOND              : angle       1.38290 (   12)
  hydrogen bonds       : bond        0.03114 (  188)
  hydrogen bonds       : angle       6.65298 (  476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1621.27 seconds
wall clock time: 28 minutes 37.30 seconds (1717.30 seconds total)