Starting phenix.real_space_refine
on Tue Feb 11 13:03:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sgy_10188/02_2025/6sgy_10188.cif"
  }
  resolution = 4.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      12      5.16       5
     C    3632      2.51       5
     N     996      2.21       5
     O    1126      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5766
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2883
          Classifications: {'peptide': 402}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360}
    Chain: "B"
      Number of atoms: 2883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2883
          Classifications: {'peptide': 402}
          Link IDs: {'PCIS': 2, 'PTRANS': 39, 'TRANS': 360}
  Time building chain proxies: 4.25, per 1000 atoms: 0.74
  Number of scatterers: 5766
  At special positions: 0
  Unit cell: (148.89, 61.683, 97.842, 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      12     16.00
     O    1126      8.00
     N     996      7.00
     C    3632      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 177 " - pdb=" SG  CYS A 376 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 177 " - pdb=" SG  CYS B 376 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 909.7 milliseconds
  

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 15 sheets defined
      17.2% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 124 through 133
    Processing helix  chain 'A' and resid 142 through 147
      removed outlier: 3.777A  pdb=" N   ILE A 146 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 244
    Processing helix  chain 'A' and resid 257 through 262
    Processing helix  chain 'A' and resid 319 through 330
    Processing helix  chain 'A' and resid 341 through 348
    Processing helix  chain 'A' and resid 463 through 471
      removed outlier: 4.100A  pdb=" N   VAL A 467 " --> pdb=" O   ASP A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 485
      removed outlier: 3.765A  pdb=" N   LEU A 484 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 124 through 133
    Processing helix  chain 'B' and resid 142 through 147
      removed outlier: 3.986A  pdb=" N   ILE B 146 " --> pdb=" O   LYS B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 244
      removed outlier: 3.577A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 264
      removed outlier: 3.746A  pdb=" N   VAL B 264 " --> pdb=" O   LEU B 260 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 330
    Processing helix  chain 'B' and resid 341 through 348
    Processing helix  chain 'B' and resid 403 through 408
      removed outlier: 3.595A  pdb=" N   THR B 406 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP B 408 " --> pdb=" O   HIS B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 471
      removed outlier: 4.105A  pdb=" N   VAL B 467 " --> pdb=" O   ASP B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 485
      removed outlier: 3.703A  pdb=" N   LEU B 484 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 105
      removed outlier: 6.678A  pdb=" N   ILE A 102 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   VAL A 141 " --> pdb=" O   ILE A 102 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ALA A 104 " --> pdb=" O   VAL A 141 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 191
    Processing sheet with id=AA4, first strand: chain 'A' and resid 230 through 232
    Processing sheet with id=AA5, first strand: chain 'A' and resid 295 through 297
    Processing sheet with id=AA6, first strand: chain 'A' and resid 408 through 409
    Processing sheet with id=AA7, first strand: chain 'A' and resid 477 through 479
      removed outlier: 4.258A  pdb=" N   LEU A 477 " --> pdb=" O   GLY A 428 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 430 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   MET A 446 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 103 through 104
    Processing sheet with id=AA9, first strand: chain 'B' and resid 112 through 115
    Processing sheet with id=AB1, first strand: chain 'B' and resid 189 through 191
    Processing sheet with id=AB2, first strand: chain 'B' and resid 189 through 191
    Processing sheet with id=AB3, first strand: chain 'B' and resid 230 through 232
    Processing sheet with id=AB4, first strand: chain 'B' and resid 315 through 317
      removed outlier: 9.350A  pdb=" N   LEU B 340 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   VAL B 297 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 409 through 410
    Processing sheet with id=AB6, first strand: chain 'B' and resid 477 through 479
      removed outlier: 4.071A  pdb=" N   LEU B 477 " --> pdb=" O   GLY B 428 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B 432 " --> pdb=" O   VAL B 479 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET B 446 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)

    170 hydrogen bonds defined for protein.
    462 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1955
        1.34 -     1.46: 1038
        1.46 -     1.57: 2899
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 5912
  Sorted by residual:
  bond pdb=" C   SER B 440 "
       pdb=" N   PRO B 441 "
    ideal  model  delta    sigma   weight residual
    1.331  1.402 -0.072 1.31e-02 5.83e+03 3.00e+01
  bond pdb=" C   SER A 440 "
       pdb=" N   PRO A 441 "
    ideal  model  delta    sigma   weight residual
    1.332  1.394 -0.062 1.32e-02 5.74e+03 2.24e+01
  bond pdb=" N   ALA A 252 "
       pdb=" CA  ALA A 252 "
    ideal  model  delta    sigma   weight residual
    1.464  1.425  0.039 9.80e-03 1.04e+04 1.60e+01
  bond pdb=" C   LEU A 288 "
       pdb=" N   PRO A 289 "
    ideal  model  delta    sigma   weight residual
    1.335  1.367 -0.032 9.40e-03 1.13e+04 1.15e+01
  bond pdb=" CB  TRP B 226 "
       pdb=" CG  TRP B 226 "
    ideal  model  delta    sigma   weight residual
    1.498  1.420  0.078 3.10e-02 1.04e+03 6.40e+00
  ... (remaining 5907 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.06: 7856
        3.06 -     6.11: 244
        6.11 -     9.17: 34
        9.17 -    12.23: 8
       12.23 -    15.29: 4
  Bond angle restraints: 8146
  Sorted by residual:
  angle pdb=" C   ALA B 160 "
        pdb=" N   PRO B 161 "
        pdb=" CA  PRO B 161 "
      ideal   model   delta    sigma   weight residual
     127.00  142.29  -15.29 2.40e+00 1.74e-01 4.06e+01
  angle pdb=" C   ALA B 160 "
        pdb=" N   PRO B 161 "
        pdb=" CD  PRO B 161 "
      ideal   model   delta    sigma   weight residual
     120.60  107.24   13.36 2.20e+00 2.07e-01 3.69e+01
  angle pdb=" N   GLY B 457 "
        pdb=" CA  GLY B 457 "
        pdb=" C   GLY B 457 "
      ideal   model   delta    sigma   weight residual
     110.42  119.33   -8.91 1.49e+00 4.50e-01 3.57e+01
  angle pdb=" N   LEU A 288 "
        pdb=" CA  LEU A 288 "
        pdb=" C   LEU A 288 "
      ideal   model   delta    sigma   weight residual
     113.25  120.06   -6.81 1.30e+00 5.92e-01 2.74e+01
  angle pdb=" N   GLU B 285 "
        pdb=" CA  GLU B 285 "
        pdb=" C   GLU B 285 "
      ideal   model   delta    sigma   weight residual
     110.91  116.88   -5.97 1.17e+00 7.31e-01 2.61e+01
  ... (remaining 8141 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.35: 3050
       17.35 -    34.69: 413
       34.69 -    52.03: 67
       52.03 -    69.38: 9
       69.38 -    86.72: 3
  Dihedral angle restraints: 3542
    sinusoidal: 1274
      harmonic: 2268
  Sorted by residual:
  dihedral pdb=" CA  ASN B 184 "
           pdb=" C   ASN B 184 "
           pdb=" N   PRO B 185 "
           pdb=" CA  PRO B 185 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  126.23   53.77     0      5.00e+00 4.00e-02 1.16e+02
  dihedral pdb=" CA  ASP A 215 "
           pdb=" C   ASP A 215 "
           pdb=" N   ALA A 216 "
           pdb=" CA  ALA A 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -133.63  -46.37     0      5.00e+00 4.00e-02 8.60e+01
  dihedral pdb=" CA  ALA B 418 "
           pdb=" C   ALA B 418 "
           pdb=" N   ASN B 419 "
           pdb=" CA  ASN B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.18  -41.82     0      5.00e+00 4.00e-02 7.00e+01
  ... (remaining 3539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 689
       0.061 -    0.122: 212
       0.122 -    0.183: 44
       0.183 -    0.244: 8
       0.244 -    0.304: 3
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CB  ILE A 190 "
            pdb=" CA  ILE A 190 "
            pdb=" CG1 ILE A 190 "
            pdb=" CG2 ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.32e+00
  chirality pdb=" CA  LEU A 288 "
            pdb=" N   LEU A 288 "
            pdb=" C   LEU A 288 "
            pdb=" CB  LEU A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  PRO A 218 "
            pdb=" N   PRO A 218 "
            pdb=" C   PRO A 218 "
            pdb=" CB  PRO A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.47    0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 953 not shown)

  Planarity restraints: 1094
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 184 "    0.071 5.00e-02 4.00e+02   1.08e-01 1.88e+01
        pdb=" N   PRO B 185 "   -0.187 5.00e-02 4.00e+02
        pdb=" CA  PRO B 185 "    0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO B 185 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 184 "   -0.062 5.00e-02 4.00e+02   9.37e-02 1.40e+01
        pdb=" N   PRO A 185 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO A 185 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 185 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 424 "    0.061 5.00e-02 4.00e+02   9.09e-02 1.32e+01
        pdb=" N   PRO A 425 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO A 425 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 425 "    0.049 5.00e-02 4.00e+02
  ... (remaining 1091 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1051
        2.76 -     3.29: 5861
        3.29 -     3.83: 10491
        3.83 -     4.36: 11088
        4.36 -     4.90: 17833
  Nonbonded interactions: 46324
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 181 "
            pdb=" OG1 THR A 188 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   ASN B 124 "
            pdb=" OG  SER B 127 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ASN A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG1 THR A 433 "
            pdb=" O   ALA A 443 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER A 450 "
            pdb=" OG1 THR A 452 "
     model   vdw
     2.274 3.040
  ... (remaining 46319 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     17.750
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6585
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      :  0.007   0.078   5912  Z= 0.460
  Angle     :  1.349  15.285   8146  Z= 0.734
  Chirality :  0.062   0.304    956
  Planarity :  0.011   0.108   1094
  Dihedral  : 15.714  86.724   2084
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.75 %
    Favored  : 87.25 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 15.17 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    Twisted General : 1.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.34 (0.24), residues: 800
  helix: -3.19 (0.27), residues: 124
  sheet: -2.86 (0.36), residues: 142
  loop : -2.98 (0.24), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 174 
 HIS   0.010   0.002   HIS A 120 
 PHE   0.025   0.003   PHE B 447 
 TYR   0.025   0.004   TYR B 307 
 ARG   0.007   0.001   ARG B 352 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  164 MET cc_start: 0.8378 (mmp) cc_final: 0.8132 (mmp)
REVERT: A  235 LEU cc_start: 0.6790 (pp) cc_final: 0.6579 (pp)
  outliers start: 2
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1846
  time to fit residues: 18.0857
Evaluate side-chains
  62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    0.1980
   chunk 60 optimal weight:    0.0020
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0670
   chunk 62 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   chunk 46 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.3126
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 208 HIS
A 316 GLN
A 419 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.082356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.062063 restraints weight = 12702.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.064564 restraints weight = 8634.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.066528 restraints weight = 6430.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.5658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5912  Z= 0.264
  Angle     :  0.903   8.841   8146  Z= 0.467
  Chirality :  0.047   0.182    956
  Planarity :  0.008   0.076   1094
  Dihedral  :  8.986  33.587    850
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.00 %
    Favored  : 94.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.25 (0.27), residues: 800
  helix: -1.79 (0.38), residues: 106
  sheet: -2.22 (0.39), residues: 148
  loop : -2.35 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 379 
 HIS   0.006   0.001   HIS B 213 
 PHE   0.012   0.002   PHE A 284 
 TYR   0.017   0.003   TYR B 112 
 ARG   0.006   0.001   ARG A 254 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8455 (m-80) cc_final: 0.8023 (m-10)
REVERT: A  118 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8575 (mm110)
REVERT: A  211 LEU cc_start: 0.8847 (pt) cc_final: 0.8405 (pt)
REVERT: A  213 HIS cc_start: 0.8615 (m-70) cc_final: 0.8082 (m-70)
REVERT: A  224 LEU cc_start: 0.9270 (tt) cc_final: 0.8958 (mt)
REVERT: A  229 LYS cc_start: 0.8928 (mtpp) cc_final: 0.8688 (mtmt)
REVERT: A  254 ARG cc_start: 0.9033 (ttm110) cc_final: 0.8208 (ttt180)
REVERT: A  446 MET cc_start: 0.8466 (tpp) cc_final: 0.8260 (tpp)
REVERT: A  477 LEU cc_start: 0.9672 (mt) cc_final: 0.9413 (tt)
REVERT: A  487 PHE cc_start: 0.9105 (m-80) cc_final: 0.8186 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1721
  time to fit residues: 17.6468
Evaluate side-chains
  71 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 20 optimal weight:    0.0060
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 50 optimal weight:    1.9990
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0970
   chunk 45 optimal weight:    0.0570
   chunk 47 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0470
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.0468
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.085747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.065667 restraints weight = 12676.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.068074 restraints weight = 8811.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.070020 restraints weight = 6659.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.6322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5912  Z= 0.235
  Angle     :  0.865   7.898   8146  Z= 0.435
  Chirality :  0.045   0.156    956
  Planarity :  0.008   0.074   1094
  Dihedral  :  8.008  30.370    850
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.44 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.28), residues: 800
  helix: -1.00 (0.41), residues: 106
  sheet: -2.24 (0.38), residues: 148
  loop : -2.05 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 379 
 HIS   0.006   0.001   HIS A 213 
 PHE   0.010   0.001   PHE A 284 
 TYR   0.011   0.002   TYR B 359 
 ARG   0.008   0.001   ARG B 455 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8552 (m-80) cc_final: 0.7890 (m-10)
REVERT: A  213 HIS cc_start: 0.8220 (m-70) cc_final: 0.7707 (m-70)
REVERT: A  224 LEU cc_start: 0.9166 (tt) cc_final: 0.8900 (mt)
REVERT: A  242 ASP cc_start: 0.9390 (t0) cc_final: 0.8580 (p0)
REVERT: A  246 LEU cc_start: 0.8996 (mt) cc_final: 0.8563 (mt)
REVERT: A  254 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8106 (ttt180)
REVERT: A  477 LEU cc_start: 0.9592 (mt) cc_final: 0.9219 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1661
  time to fit residues: 16.2887
Evaluate side-chains
  73 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0370
   chunk 59 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.5258
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN
A 166 GLN
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.085294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.065379 restraints weight = 13148.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067694 restraints weight = 9244.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.069629 restraints weight = 7090.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.6600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5912  Z= 0.237
  Angle     :  0.833   9.219   8146  Z= 0.418
  Chirality :  0.045   0.134    956
  Planarity :  0.007   0.072   1094
  Dihedral  :  7.434  29.745    850
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.28), residues: 800
  helix: -0.73 (0.41), residues: 106
  sheet: -2.10 (0.38), residues: 144
  loop : -1.95 (0.27), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 448 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.010   0.002   PHE A 487 
 TYR   0.010   0.002   TYR A 359 
 ARG   0.002   0.000   ARG A 254 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8603 (m-80) cc_final: 0.7910 (m-10)
REVERT: A  213 HIS cc_start: 0.8132 (m-70) cc_final: 0.7614 (m-70)
REVERT: A  224 LEU cc_start: 0.9239 (tt) cc_final: 0.8926 (mt)
REVERT: A  242 ASP cc_start: 0.9396 (t0) cc_final: 0.8595 (p0)
REVERT: A  246 LEU cc_start: 0.8996 (mt) cc_final: 0.8615 (mt)
REVERT: A  254 ARG cc_start: 0.8809 (ttm110) cc_final: 0.8355 (ttt180)
REVERT: A  308 TYR cc_start: 0.8856 (m-80) cc_final: 0.8612 (m-80)
REVERT: A  446 MET cc_start: 0.8006 (tpp) cc_final: 0.7759 (tpp)
REVERT: A  455 ARG cc_start: 0.8863 (pmt170) cc_final: 0.8389 (ptt-90)
REVERT: A  477 LEU cc_start: 0.9520 (mt) cc_final: 0.9151 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.2002
  time to fit residues: 19.8416
Evaluate side-chains
  66 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0870
   chunk 22 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0570
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0020
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.6086
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.085154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.065574 restraints weight = 13030.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.067935 restraints weight = 9124.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.069805 restraints weight = 6892.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.6963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5912  Z= 0.240
  Angle     :  0.821   7.844   8146  Z= 0.416
  Chirality :  0.045   0.131    956
  Planarity :  0.008   0.072   1094
  Dihedral  :  7.209  28.373    850
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.61 (0.28), residues: 800
  helix: -0.38 (0.42), residues: 106
  sheet: -2.17 (0.37), residues: 146
  loop : -1.99 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 448 
 HIS   0.004   0.001   HIS B 405 
 PHE   0.008   0.001   PHE B 487 
 TYR   0.009   0.002   TYR B 429 
 ARG   0.004   0.001   ARG A 163 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.8289 (m-80) cc_final: 0.7972 (m-10)
REVERT: A  118 GLN cc_start: 0.8452 (tp-100) cc_final: 0.7815 (tp40)
REVERT: A  131 ILE cc_start: 0.9253 (mm) cc_final: 0.8853 (mm)
REVERT: A  175 THR cc_start: 0.8841 (p) cc_final: 0.8590 (p)
REVERT: A  211 LEU cc_start: 0.8556 (pt) cc_final: 0.8313 (pt)
REVERT: A  213 HIS cc_start: 0.8102 (m-70) cc_final: 0.7628 (m90)
REVERT: A  224 LEU cc_start: 0.9263 (tt) cc_final: 0.8981 (mt)
REVERT: A  254 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8213 (ttt180)
REVERT: A  308 TYR cc_start: 0.8898 (m-80) cc_final: 0.8503 (m-80)
REVERT: A  446 MET cc_start: 0.8030 (tpp) cc_final: 0.7736 (tpp)
REVERT: A  455 ARG cc_start: 0.8837 (pmt170) cc_final: 0.8586 (ptt-90)
REVERT: A  495 ARG cc_start: 0.8961 (tpt90) cc_final: 0.8615 (tpm170)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1595
  time to fit residues: 14.9617
Evaluate side-chains
  66 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0170
   chunk 44 optimal weight:    0.0070
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0020
   chunk 36 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0020
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.0852
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.088611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.068167 restraints weight = 12837.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.070728 restraints weight = 8906.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.072807 restraints weight = 6713.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.7307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5912  Z= 0.216
  Angle     :  0.808   8.785   8146  Z= 0.401
  Chirality :  0.044   0.135    956
  Planarity :  0.007   0.070   1094
  Dihedral  :  6.706  25.973    850
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.28), residues: 800
  helix:  0.07 (0.45), residues: 106
  sheet: -2.18 (0.35), residues: 146
  loop : -2.04 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 379 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.011   0.002   PHE B 487 
 TYR   0.010   0.002   TYR B 112 
 ARG   0.009   0.001   ARG B 151 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.7966 (m-80) cc_final: 0.7684 (m-10)
REVERT: A  213 HIS cc_start: 0.7996 (m-70) cc_final: 0.7603 (m90)
REVERT: A  254 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8443 (ttt180)
REVERT: A  308 TYR cc_start: 0.8855 (m-80) cc_final: 0.8465 (m-80)
REVERT: A  446 MET cc_start: 0.7994 (tpp) cc_final: 0.7672 (tpp)
REVERT: A  455 ARG cc_start: 0.8776 (pmt170) cc_final: 0.8467 (pmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1786
  time to fit residues: 17.2937
Evaluate side-chains
  67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 3 optimal weight:    0.0470
   chunk 71 optimal weight:    0.3980
   chunk 57 optimal weight:    0.3980
   chunk 49 optimal weight:    0.0060
   chunk 42 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0770
   overall best weight:    0.1852
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 362 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.089030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.068252 restraints weight = 12446.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.070833 restraints weight = 8610.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.072853 restraints weight = 6485.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.7781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5912  Z= 0.218
  Angle     :  0.825   8.653   8146  Z= 0.411
  Chirality :  0.045   0.134    956
  Planarity :  0.007   0.070   1094
  Dihedral  :  6.641  31.115    850
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  1.00 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.49 (0.28), residues: 800
  helix:  0.07 (0.45), residues: 106
  sheet: -2.17 (0.37), residues: 146
  loop : -1.97 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 379 
 HIS   0.007   0.002   HIS A 378 
 PHE   0.009   0.001   PHE A 487 
 TYR   0.010   0.001   TYR B 359 
 ARG   0.005   0.000   ARG A 151 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.7979 (m-80) cc_final: 0.7446 (m-10)
REVERT: A  131 ILE cc_start: 0.9402 (mm) cc_final: 0.9135 (mm)
REVERT: A  197 ASP cc_start: 0.7928 (t0) cc_final: 0.7466 (p0)
REVERT: A  211 LEU cc_start: 0.8347 (pt) cc_final: 0.8127 (pt)
REVERT: A  213 HIS cc_start: 0.8009 (m-70) cc_final: 0.7607 (m90)
REVERT: A  254 ARG cc_start: 0.8778 (ttm110) cc_final: 0.8501 (ttt180)
REVERT: A  308 TYR cc_start: 0.8871 (m-80) cc_final: 0.8400 (m-80)
REVERT: A  350 MET cc_start: 0.8319 (mmp) cc_final: 0.7542 (mmm)
REVERT: A  400 LEU cc_start: 0.8699 (mp) cc_final: 0.8329 (pp)
REVERT: A  446 MET cc_start: 0.7959 (tpp) cc_final: 0.7720 (tpp)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1750
  time to fit residues: 17.4973
Evaluate side-chains
  67 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.0010
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0020
   chunk 77 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 12 optimal weight:    0.0980
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.2594
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.090193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.070348 restraints weight = 12565.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.072989 restraints weight = 8750.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.075026 restraints weight = 6583.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.7854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   5912  Z= 0.222
  Angle     :  0.806   8.938   8146  Z= 0.399
  Chirality :  0.044   0.133    956
  Planarity :  0.007   0.069   1094
  Dihedral  :  6.418  28.449    850
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.28), residues: 800
  helix: -0.05 (0.43), residues: 106
  sheet: -2.13 (0.35), residues: 166
  loop : -2.02 (0.27), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.009   0.001   PHE A 284 
 TYR   0.008   0.001   TYR A 429 
 ARG   0.006   0.001   ARG A 238 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.7924 (m-80) cc_final: 0.7567 (m-10)
REVERT: A  211 LEU cc_start: 0.8543 (pt) cc_final: 0.8072 (tp)
REVERT: A  213 HIS cc_start: 0.8000 (m-70) cc_final: 0.7648 (m90)
REVERT: A  254 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8503 (ttt180)
REVERT: A  261 PHE cc_start: 0.8950 (t80) cc_final: 0.8744 (t80)
REVERT: A  308 TYR cc_start: 0.8816 (m-80) cc_final: 0.8335 (m-80)
REVERT: A  446 MET cc_start: 0.7948 (tpp) cc_final: 0.7642 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1593
  time to fit residues: 15.4828
Evaluate side-chains
  66 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:    0.0870
   chunk 12 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   chunk 40 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0980
   overall best weight:    0.4380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.089500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.068793 restraints weight = 12301.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.071451 restraints weight = 8463.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.073578 restraints weight = 6331.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.8086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5912  Z= 0.220
  Angle     :  0.816   9.228   8146  Z= 0.397
  Chirality :  0.045   0.241    956
  Planarity :  0.007   0.069   1094
  Dihedral  :  6.320  26.995    850
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.29), residues: 800
  helix:  0.42 (0.46), residues: 106
  sheet: -2.05 (0.37), residues: 150
  loop : -1.90 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.011   0.001   PHE B 487 
 TYR   0.010   0.001   TYR B 359 
 ARG   0.006   0.001   ARG B 238 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  112 TYR cc_start: 0.7998 (m-80) cc_final: 0.7613 (m-10)
REVERT: A  197 ASP cc_start: 0.7838 (t70) cc_final: 0.7603 (t0)
REVERT: A  213 HIS cc_start: 0.7970 (m-70) cc_final: 0.7642 (m90)
REVERT: A  242 ASP cc_start: 0.9304 (t0) cc_final: 0.8600 (p0)
REVERT: A  246 LEU cc_start: 0.9079 (mt) cc_final: 0.8825 (mt)
REVERT: A  254 ARG cc_start: 0.8871 (ttm110) cc_final: 0.8563 (ttt180)
REVERT: A  308 TYR cc_start: 0.8855 (m-80) cc_final: 0.8392 (m-80)
REVERT: A  446 MET cc_start: 0.8057 (tpp) cc_final: 0.7822 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1589
  time to fit residues: 14.8665
Evaluate side-chains
  62 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0870
   chunk 72 optimal weight:    0.0770
   chunk 64 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0270
   chunk 32 optimal weight:    5.9990
   overall best weight:    0.1974
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.091699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.071105 restraints weight = 12501.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.073671 restraints weight = 8821.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.075728 restraints weight = 6704.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.8357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5912  Z= 0.213
  Angle     :  0.822  10.652   8146  Z= 0.394
  Chirality :  0.045   0.175    956
  Planarity :  0.006   0.061   1094
  Dihedral  :  5.984  25.575    850
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.29), residues: 800
  helix:  0.48 (0.47), residues: 106
  sheet: -1.95 (0.37), residues: 150
  loop : -1.84 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 174 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.012   0.002   PHE B 284 
 TYR   0.011   0.001   TYR B 359 
 ARG   0.005   0.001   ARG B 238 

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

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

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1600 Ramachandran restraints generated.
    800 Oldfield, 0 Emsley, 800 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.8619 (mt) cc_final: 0.8381 (mt)
REVERT: A  197 ASP cc_start: 0.7607 (t70) cc_final: 0.7373 (t0)
REVERT: A  211 LEU cc_start: 0.8591 (pt) cc_final: 0.8182 (tp)
REVERT: A  213 HIS cc_start: 0.7935 (m-70) cc_final: 0.7625 (m90)
REVERT: A  215 ASP cc_start: 0.8347 (t70) cc_final: 0.8102 (t0)
REVERT: A  254 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8541 (ttt180)
REVERT: A  308 TYR cc_start: 0.8854 (m-80) cc_final: 0.8328 (m-80)
REVERT: A  451 ASP cc_start: 0.9283 (p0) cc_final: 0.8911 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1683
  time to fit residues: 16.2451
Evaluate side-chains
  65 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    0.0370
   chunk 22 optimal weight:    0.0870
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    0.2980
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0060
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0000
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.0856
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.091421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.070622 restraints weight = 12194.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.073126 restraints weight = 8583.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.075143 restraints weight = 6551.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.8578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   5912  Z= 0.214
  Angle     :  0.840   9.585   8146  Z= 0.401
  Chirality :  0.045   0.162    956
  Planarity :  0.007   0.063   1094
  Dihedral  :  5.988  28.363    850
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.17 (0.29), residues: 800
  helix:  0.40 (0.48), residues: 106
  sheet: -1.84 (0.38), residues: 146
  loop : -1.81 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 174 
 HIS   0.006   0.001   HIS B 120 
 PHE   0.011   0.002   PHE B 284 
 TYR   0.012   0.001   TYR B 112 
 ARG   0.005   0.000   ARG A 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1669.99 seconds
wall clock time: 30 minutes 47.65 seconds (1847.65 seconds total)