Starting phenix.real_space_refine
on Thu Mar  6 09:45:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6sgy_10188/03_2025/6sgy_10188.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6sgy_10188/03_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_10188/03_2025/6sgy_10188.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6sgy_10188/03_2025/6sgy_10188.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6sgy_10188/03_2025/6sgy_10188.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6sgy_10188/03_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-5624/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: 3.97, per 1000 atoms: 0.69
  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: 1.23
  Conformation dependent library (CDL) restraints added in 834.8 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: 0.71
  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: 1.63

  Time building geometry restraints manager: 1.49 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:             1.720
  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:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     16.730
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  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:2.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.420
-------------------------------------------------------------------------------
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  : 0.276 
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: 0.1746
  time to fit residues: 17.2264
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  : 0.303 
-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.082360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.062135 restraints weight = 12959.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.064538 restraints weight = 8864.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.066570 restraints weight = 6625.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.5655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5912  Z= 0.266
  Angle     :  0.902   8.853   8146  Z= 0.467
  Chirality :  0.047   0.179    956
  Planarity :  0.008   0.076   1094
  Dihedral  :  8.991  33.626    850
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.75 %
    Favored  : 90.25 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  5.33 %
    Favored  : 94.33 %
  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: -1.80 (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   0.018   0.003   TYR B 112 
 ARG   0.006   0.001   ARG B 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  : 0.286 
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: 0.8459 (m-80) cc_final: 0.8028 (m-10)
REVERT: A  118 GLN cc_start: 0.8885 (mm-40) cc_final: 0.8576 (mm110)
REVERT: A  211 LEU cc_start: 0.8847 (pt) cc_final: 0.8403 (pt)
REVERT: A  213 HIS cc_start: 0.8625 (m-70) cc_final: 0.8067 (m-70)
REVERT: A  224 LEU cc_start: 0.9269 (tt) cc_final: 0.8955 (mt)
REVERT: A  229 LYS cc_start: 0.8927 (mtpp) cc_final: 0.8688 (mtmt)
REVERT: A  254 ARG cc_start: 0.9031 (ttm110) cc_final: 0.8220 (ttt180)
REVERT: A  446 MET cc_start: 0.8473 (tpp) cc_final: 0.8269 (tpp)
REVERT: A  477 LEU cc_start: 0.9674 (mt) cc_final: 0.9416 (tt)
REVERT: A  487 PHE cc_start: 0.9103 (m-80) cc_final: 0.8191 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1632
  time to fit residues: 16.7950
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  : 0.294 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 20 optimal weight:    0.0870
   chunk 74 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0370
   chunk 47 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.5236
-------------------------------------------------------------------------------
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 = 0.3485 r_free = 0.3485 target = 0.082585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.063070 restraints weight = 12895.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.065389 restraints weight = 8976.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.067097 restraints weight = 6792.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.6168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5912  Z= 0.237
  Angle     :  0.855   7.480   8146  Z= 0.435
  Chirality :  0.045   0.158    956
  Planarity :  0.008   0.074   1094
  Dihedral  :  8.173  31.106    850
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.25 %
    Favored  : 89.75 %
  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: -2.92 (0.28), residues: 800
  helix: -1.26 (0.38), residues: 106
  sheet: -2.30 (0.38), residues: 148
  loop : -2.07 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 448 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.009   0.001   PHE A 284 
 TYR   0.012   0.003   TYR B 359 
 ARG   0.014   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
  81 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.283 
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: A  112 TYR cc_start: 0.8638 (m-80) cc_final: 0.7524 (m-10)
REVERT: A  211 LEU cc_start: 0.8712 (pt) cc_final: 0.8362 (pt)
REVERT: A  213 HIS cc_start: 0.8347 (m-70) cc_final: 0.7812 (m-70)
REVERT: A  224 LEU cc_start: 0.9250 (tt) cc_final: 0.8932 (mt)
REVERT: A  229 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8755 (mtmt)
REVERT: A  254 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8154 (ttt180)
REVERT: A  477 LEU cc_start: 0.9672 (mt) cc_final: 0.9359 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1693
  time to fit residues: 16.2550
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  : 0.311 
-------------------------------------------------------------------------------
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:    0.0040
   chunk 57 optimal weight:    0.5980
   chunk 49 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0050
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4206
-------------------------------------------------------------------------------
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 = 0.3498 r_free = 0.3498 target = 0.083907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.064120 restraints weight = 13195.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.066412 restraints weight = 9173.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.068353 restraints weight = 6974.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.6533

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= 0.232
  Angle     :  0.839   9.182   8146  Z= 0.422
  Chirality :  0.044   0.133    956
  Planarity :  0.007   0.073   1094
  Dihedral  :  7.582  29.692    850
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 13.63
  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: -2.63 (0.28), residues: 800
  helix: -0.64 (0.41), residues: 106
  sheet: -2.27 (0.37), residues: 148
  loop : -1.91 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 379 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.010   0.002   PHE B 487 
 TYR   0.013   0.002   TYR B 112 
 ARG   0.003   0.001   ARG B 151 

*********************** 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  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.8601 (pt) cc_final: 0.8284 (pt)
REVERT: A  213 HIS cc_start: 0.8181 (m-70) cc_final: 0.7644 (m-70)
REVERT: A  224 LEU cc_start: 0.9250 (tt) cc_final: 0.8983 (mt)
REVERT: A  229 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8649 (mtmt)
REVERT: A  242 ASP cc_start: 0.9409 (t0) cc_final: 0.8613 (p0)
REVERT: A  246 LEU cc_start: 0.9085 (mt) cc_final: 0.8729 (mt)
REVERT: A  254 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8400 (ttt180)
REVERT: A  308 TYR cc_start: 0.9002 (m-80) cc_final: 0.8618 (m-80)
REVERT: A  446 MET cc_start: 0.8033 (tpp) cc_final: 0.7798 (tpp)
REVERT: A  455 ARG cc_start: 0.8864 (pmt170) cc_final: 0.8412 (ptt-90)
REVERT: A  477 LEU cc_start: 0.9578 (mt) cc_final: 0.9229 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1486
  time to fit residues: 14.9740
Evaluate side-chains
  72 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 47 optimal weight:    0.0870
   chunk 31 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0050
   chunk 6 optimal weight:    0.0170
   chunk 22 optimal weight:    0.8980
   chunk 68 optimal weight:    0.0040
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0010
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.0228
-------------------------------------------------------------------------------
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 = 0.3558 r_free = 0.3558 target = 0.087604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.067841 restraints weight = 12918.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.070095 restraints weight = 9229.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.072039 restraints weight = 7112.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.7002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5912  Z= 0.223
  Angle     :  0.830   9.121   8146  Z= 0.409
  Chirality :  0.045   0.135    956
  Planarity :  0.007   0.071   1094
  Dihedral  :  6.897  26.963    850
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.25 %
    Favored  : 90.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  3.33 %
    Favored  : 96.33 %
  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: -2.51 (0.28), residues: 800
  helix: -0.16 (0.45), residues: 106
  sheet: -2.19 (0.36), residues: 146
  loop : -1.92 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 379 
 HIS   0.005   0.001   HIS A 213 
 PHE   0.012   0.002   PHE B 487 
 TYR   0.009   0.001   TYR B 359 
 ARG   0.002   0.001   ARG A 352 

*********************** 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
  81 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8270 (tp40)
REVERT: A  213 HIS cc_start: 0.8073 (m-70) cc_final: 0.7636 (m90)
REVERT: A  254 ARG cc_start: 0.9017 (ttm110) cc_final: 0.8294 (ttt180)
REVERT: A  308 TYR cc_start: 0.9014 (m-80) cc_final: 0.8703 (m-80)
REVERT: A  446 MET cc_start: 0.8047 (tpp) cc_final: 0.7483 (tpp)
REVERT: A  455 ARG cc_start: 0.8806 (pmt170) cc_final: 0.8592 (ptt-90)
REVERT: A  477 LEU cc_start: 0.9465 (mt) cc_final: 0.9224 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.1303
  time to fit residues: 12.8759
Evaluate side-chains
  70 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 14 optimal weight:    0.0970
   chunk 44 optimal weight:    0.0870
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0040
   chunk 70 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.3168
-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.087581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.067297 restraints weight = 13008.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.069633 restraints weight = 9117.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.071607 restraints weight = 6961.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.7146

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= 0.207
  Angle     :  0.818  11.766   8146  Z= 0.403
  Chirality :  0.044   0.134    956
  Planarity :  0.007   0.071   1094
  Dihedral  :  6.711  28.804    850
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 10.92
  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: -2.47 (0.28), residues: 800
  helix: -0.11 (0.44), residues: 106
  sheet: -2.19 (0.36), residues: 150
  loop : -1.88 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 379 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.009   0.001   PHE B 487 
 TYR   0.010   0.002   TYR B 359 
 ARG   0.003   0.000   ARG A 230 

*********************** 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
  81 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 THR cc_start: 0.8789 (p) cc_final: 0.8523 (p)
REVERT: A  211 LEU cc_start: 0.8460 (pt) cc_final: 0.8183 (pt)
REVERT: A  213 HIS cc_start: 0.8031 (m-70) cc_final: 0.7626 (m90)
REVERT: A  229 LYS cc_start: 0.9258 (ttmt) cc_final: 0.9032 (tmmt)
REVERT: A  254 ARG cc_start: 0.8830 (ttm110) cc_final: 0.8466 (ttt180)
REVERT: A  308 TYR cc_start: 0.8920 (m-80) cc_final: 0.8516 (m-80)
REVERT: A  446 MET cc_start: 0.8007 (tpp) cc_final: 0.7792 (tpp)
REVERT: A  477 LEU cc_start: 0.9419 (mt) cc_final: 0.9178 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1318
  time to fit residues: 13.0583
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  : 0.281 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 71 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0030
   chunk 49 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0060
   chunk 54 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.2406
-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.089404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.069572 restraints weight = 13451.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.072031 restraints weight = 9470.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.073946 restraints weight = 7237.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.7491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5912  Z= 0.204
  Angle     :  0.792   8.033   8146  Z= 0.392
  Chirality :  0.044   0.134    956
  Planarity :  0.006   0.070   1094
  Dihedral  :  6.492  29.191    850
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  1.67 %
    Favored  : 98.00 %
  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: -2.38 (0.29), residues: 800
  helix:  0.04 (0.44), residues: 106
  sheet: -2.08 (0.38), residues: 150
  loop : -1.85 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 379 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.010   0.001   PHE A 487 
 TYR   0.010   0.001   TYR B 359 
 ARG   0.002   0.000   ARG A 455 

*********************** 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
  80 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 LEU cc_start: 0.8514 (pt) cc_final: 0.8017 (tp)
REVERT: A  213 HIS cc_start: 0.8027 (m-70) cc_final: 0.7653 (m90)
REVERT: A  254 ARG cc_start: 0.8732 (ttm110) cc_final: 0.8461 (ttt180)
REVERT: A  308 TYR cc_start: 0.8833 (m-80) cc_final: 0.8372 (m-80)
REVERT: A  350 MET cc_start: 0.8368 (mmp) cc_final: 0.7338 (mmm)
REVERT: A  446 MET cc_start: 0.7947 (tpp) cc_final: 0.7626 (tpp)
REVERT: A  477 LEU cc_start: 0.9378 (mt) cc_final: 0.9091 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1371
  time to fit residues: 13.4998
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  : 0.309 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 11 optimal weight:    0.0270
   chunk 3 optimal weight:    0.0070
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0030
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.0262
-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.090439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.069892 restraints weight = 12466.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.072498 restraints weight = 8655.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.074497 restraints weight = 6560.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.7705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5912  Z= 0.210
  Angle     :  0.814   8.648   8146  Z= 0.401
  Chirality :  0.045   0.193    956
  Planarity :  0.006   0.068   1094
  Dihedral  :  6.337  31.261    850
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  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 : 0.28 %

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: -2.18 (0.29), residues: 800
  helix:  0.23 (0.46), residues: 106
  sheet: -1.54 (0.44), residues: 112
  loop : -1.89 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 379 
 HIS   0.006   0.001   HIS A 378 
 PHE   0.011   0.002   PHE A 284 
 TYR   0.005   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
  79 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8468 (mm-40) cc_final: 0.8091 (tp40)
REVERT: A  211 LEU cc_start: 0.8541 (pt) cc_final: 0.8050 (tp)
REVERT: A  213 HIS cc_start: 0.7984 (m-70) cc_final: 0.7586 (m90)
REVERT: A  254 ARG cc_start: 0.8798 (ttm110) cc_final: 0.8525 (ttt180)
REVERT: A  308 TYR cc_start: 0.8831 (m-80) cc_final: 0.8343 (m-80)
REVERT: A  359 TYR cc_start: 0.8801 (m-80) cc_final: 0.8383 (m-80)
REVERT: A  446 MET cc_start: 0.7862 (tpp) cc_final: 0.7531 (tpp)
REVERT: A  477 LEU cc_start: 0.9277 (mt) cc_final: 0.8906 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1800
  time to fit residues: 17.5910
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  : 0.286 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 12 optimal weight:    0.0970
   chunk 11 optimal weight:    0.0370
   chunk 73 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 40 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0070
   chunk 0 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0770
   overall best weight:    0.0632
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
A 219 ASN
A 378 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.092057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.071760 restraints weight = 12656.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.074264 restraints weight = 8918.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.076295 restraints weight = 6766.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.7980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   5912  Z= 0.225
  Angle     :  0.807   8.973   8146  Z= 0.395
  Chirality :  0.045   0.164    956
  Planarity :  0.007   0.068   1094
  Dihedral  :  6.115  29.969    850
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  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: -2.27 (0.28), residues: 800
  helix:  0.27 (0.46), residues: 108
  sheet: -1.58 (0.46), residues: 112
  loop : -1.99 (0.25), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 448 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.010   0.002   PHE A 487 
 TYR   0.008   0.001   TYR B 112 
 ARG   0.007   0.001   ARG B 163 

*********************** 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
  82 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8137 (tp40)
REVERT: A  211 LEU cc_start: 0.8486 (pt) cc_final: 0.8026 (tp)
REVERT: A  213 HIS cc_start: 0.7810 (m-70) cc_final: 0.7567 (m90)
REVERT: A  254 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8517 (ttt180)
REVERT: A  308 TYR cc_start: 0.8809 (m-80) cc_final: 0.8328 (m-80)
REVERT: A  446 MET cc_start: 0.7754 (tpp) cc_final: 0.7404 (tpp)
REVERT: A  477 LEU cc_start: 0.9183 (mt) cc_final: 0.8866 (tt)
REVERT: A  486 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8407 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1470
  time to fit residues: 14.5108
Evaluate side-chains
  63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 1 optimal weight:    0.0670
   chunk 70 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 61 optimal weight:    0.0270
   chunk 32 optimal weight:    0.1980
   overall best weight:    0.2976
-------------------------------------------------------------------------------
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 = 0.3619 r_free = 0.3619 target = 0.091311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.070544 restraints weight = 13082.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.073033 restraints weight = 9349.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.075024 restraints weight = 7169.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
moved from start:          0.8060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5912  Z= 0.209
  Angle     :  0.809  10.135   8146  Z= 0.390
  Chirality :  0.044   0.171    956
  Planarity :  0.006   0.067   1094
  Dihedral  :  6.007  28.842    850
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.00 %
    Favored  : 99.00 %
  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: -2.08 (0.29), residues: 800
  helix:  0.57 (0.48), residues: 106
  sheet: -1.39 (0.46), residues: 112
  loop : -1.90 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 379 
 HIS   0.003   0.001   HIS B 213 
 PHE   0.008   0.001   PHE B 284 
 TYR   0.007   0.001   TYR A 429 
 ARG   0.006   0.001   ARG A 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
  77 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.9052 (mp) cc_final: 0.8807 (mp)
REVERT: A  211 LEU cc_start: 0.8595 (pt) cc_final: 0.8166 (tp)
REVERT: A  213 HIS cc_start: 0.7956 (m-70) cc_final: 0.7622 (m90)
REVERT: A  242 ASP cc_start: 0.9236 (t0) cc_final: 0.8520 (p0)
REVERT: A  246 LEU cc_start: 0.9021 (mt) cc_final: 0.8760 (mt)
REVERT: A  254 ARG cc_start: 0.8790 (ttm110) cc_final: 0.8562 (ttt180)
REVERT: A  261 PHE cc_start: 0.9084 (t80) cc_final: 0.8860 (t80)
REVERT: A  308 TYR cc_start: 0.8851 (m-80) cc_final: 0.8351 (m-80)
REVERT: A  446 MET cc_start: 0.7898 (tpp) cc_final: 0.7568 (tpp)
REVERT: A  477 LEU cc_start: 0.9249 (mt) cc_final: 0.8920 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1174
  time to fit residues: 11.2768
Evaluate side-chains
  63 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 22 optimal weight:    0.0070
   chunk 4 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0170
   chunk 2 optimal weight:    0.4980
   chunk 38 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0570
   chunk 11 optimal weight:    0.0670
   chunk 34 optimal weight:    0.0030
   overall best weight:    0.0302
-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.093712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.072478 restraints weight = 11789.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.075164 restraints weight = 8244.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.077260 restraints weight = 6190.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.8348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5912  Z= 0.204
  Angle     :  0.814   9.769   8146  Z= 0.388
  Chirality :  0.044   0.133    956
  Planarity :  0.006   0.064   1094
  Dihedral  :  5.679  27.985    850
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  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: -2.20 (0.29), residues: 800
  helix:  0.42 (0.48), residues: 108
  sheet: -1.46 (0.43), residues: 136
  loop : -1.97 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 379 
 HIS   0.004   0.001   HIS B 213 
 PHE   0.012   0.002   PHE A 284 
 TYR   0.007   0.001   TYR A 112 
 ARG   0.006   0.000   ARG B 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1723.72 seconds
wall clock time: 30 minutes 54.92 seconds (1854.92 seconds total)