Starting phenix.real_space_refine
on Sat Aug 23 10:36:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uq6_42462/08_2025/8uq6_42462.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    3734      2.51       5
     N    1073      2.21       5
     O    1147      1.98       5
     H    5689      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 765, 11700
          Classifications: {'peptide': 765}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 6, 'PTRANS': 58, 'TRANS': 700}
          Chain breaks: 1
  Time building chain proxies: 1.57, per 1000 atoms: 0.13
  Number of scatterers: 11700
  At special positions: 0
  Unit cell: (80.311, 97.02, 111.034, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      57     16.00
     O    1147      8.00
     N    1073      7.00
     C    3734      6.00
     H    5689      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 248.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      6.7% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 67 through 70
      removed outlier: 3.787A  pdb=" N   GLU A  70 " --> pdb=" O   HIS A  67 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 67 through 70'
    Processing helix  chain 'A' and resid 96 through 101
    Processing helix  chain 'A' and resid 224 through 228
      removed outlier: 3.778A  pdb=" N   LYS A 227 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.648A  pdb=" N   THR A 303 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 412 through 416
    Processing helix  chain 'A' and resid 517 through 521
    Processing helix  chain 'A' and resid 796 through 798
      No H-bonds generated for 'chain 'A' and resid 796 through 798'
    Processing helix  chain 'A' and resid 799 through 804
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 42
    Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 245
    Processing sheet with id=AA4, first strand: chain 'A' and resid 438 through 441
      removed outlier: 5.538A  pdb=" N   THR A 439 " --> pdb=" O   TRP A 446 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   TRP A 446 " --> pdb=" O   THR A 439 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 441 " --> pdb=" O   VAL A 444 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 495 through 496
    Processing sheet with id=AA6, first strand: chain 'A' and resid 542 through 543
    Processing sheet with id=AA7, first strand: chain 'A' and resid 617 through 619
    Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 703
    Processing sheet with id=AA9, first strand: chain 'A' and resid 763 through 766
      removed outlier: 5.655A  pdb=" N   LEU A 764 " --> pdb=" O   GLN A 775 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN A 775 " --> pdb=" O   LEU A 764 " (cutoff:3.500A)

    51 hydrogen bonds defined for protein.
    90 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: 2.23

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        0.95 -     1.13: 5682
        1.13 -     1.30: 1093
        1.30 -     1.48: 2438
        1.48 -     1.66: 2593
        1.66 -     1.84: 67
  Bond restraints: 11873
  Sorted by residual:
  bond pdb=" CE3 TRP A 299 "
       pdb=" HE3 TRP A 299 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.70e+01
  bond pdb=" N   SER A 292 "
       pdb=" H   SER A 292 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CH2 TRP A 244 "
       pdb=" HH2 TRP A 244 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CE2 PHE A 658 "
       pdb=" HE2 PHE A 658 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.66e+01
  bond pdb=" N   TYR A 633 "
       pdb=" H   TYR A 633 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 11868 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.37: 21159
        7.37 -    14.74: 257
       14.74 -    22.10: 1
       22.10 -    29.47: 4
       29.47 -    36.84: 5
  Bond angle restraints: 21426
  Sorted by residual:
  angle pdb=" C   ARG A 386 "
        pdb=" CA  ARG A 386 "
        pdb=" HA  ARG A 386 "
      ideal   model   delta    sigma   weight residual
     109.00   72.16   36.84 3.00e+00 1.11e-01 1.51e+02
  angle pdb=" N   TYR A 385 "
        pdb=" CA  TYR A 385 "
        pdb=" HA  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     110.00   73.80   36.20 3.00e+00 1.11e-01 1.46e+02
  angle pdb=" N   ASN A 450 "
        pdb=" CA  ASN A 450 "
        pdb=" HA  ASN A 450 "
      ideal   model   delta    sigma   weight residual
     110.00   74.61   35.39 3.00e+00 1.11e-01 1.39e+02
  angle pdb=" C   TYR A 385 "
        pdb=" CA  TYR A 385 "
        pdb=" HA  TYR A 385 "
      ideal   model   delta    sigma   weight residual
     109.00   75.27   33.73 3.00e+00 1.11e-01 1.26e+02
  angle pdb=" C   ASN A 450 "
        pdb=" CA  ASN A 450 "
        pdb=" HA  ASN A 450 "
      ideal   model   delta    sigma   weight residual
     109.00   77.16   31.84 3.00e+00 1.11e-01 1.13e+02
  ... (remaining 21421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 4828
       16.45 -    32.89: 580
       32.89 -    49.34: 167
       49.34 -    65.79: 104
       65.79 -    82.23: 15
  Dihedral angle restraints: 5694
    sinusoidal: 3086
      harmonic: 2608
  Sorted by residual:
  dihedral pdb=" C   ARG A 386 "
           pdb=" N   ARG A 386 "
           pdb=" CA  ARG A 386 "
           pdb=" CB  ARG A 386 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.39   16.79     0      2.50e+00 1.60e-01 4.51e+01
  dihedral pdb=" C   TYR A 385 "
           pdb=" N   TYR A 385 "
           pdb=" CA  TYR A 385 "
           pdb=" CB  TYR A 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.69   15.09     0      2.50e+00 1.60e-01 3.64e+01
  dihedral pdb=" CA  GLN A 297 "
           pdb=" C   GLN A 297 "
           pdb=" N   HIS A 298 "
           pdb=" CA  HIS A 298 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.45   29.55     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 5691 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 641
       0.137 -    0.274: 194
       0.274 -    0.410: 26
       0.410 -    0.547: 3
       0.547 -    0.684: 4
  Chirality restraints: 868
  Sorted by residual:
  chirality pdb=" CA  ARG A 386 "
            pdb=" N   ARG A 386 "
            pdb=" C   ARG A 386 "
            pdb=" CB  ARG A 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.83    0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" CA  TYR A 385 "
            pdb=" N   TYR A 385 "
            pdb=" C   TYR A 385 "
            pdb=" CB  TYR A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.10e+01
  chirality pdb=" CA  ASN A 450 "
            pdb=" N   ASN A 450 "
            pdb=" C   ASN A 450 "
            pdb=" CB  ASN A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.87    0.64 2.00e-01 2.50e+01 1.02e+01
  ... (remaining 865 not shown)

  Planarity restraints: 1816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  62 "    0.051 9.50e-02 1.11e+02   1.82e-01 7.40e+02
        pdb=" NE  ARG A  62 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  62 "    0.042 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  62 "    0.190 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  62 "   -0.027 2.00e-02 2.50e+03
        pdb="HH11 ARG A  62 "    0.103 2.00e-02 2.50e+03
        pdb="HH12 ARG A  62 "   -0.390 2.00e-02 2.50e+03
        pdb="HH21 ARG A  62 "   -0.145 2.00e-02 2.50e+03
        pdb="HH22 ARG A  62 "    0.267 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 446 "   -0.329 2.00e-02 2.50e+03   1.14e-01 5.18e+02
        pdb=" CG  TRP A 446 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 446 "    0.088 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 446 "    0.030 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 446 "    0.107 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 446 "    0.018 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 446 "    0.061 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 446 "   -0.072 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 446 "    0.042 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 446 "   -0.049 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 446 "    0.044 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 446 "    0.101 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 446 "    0.123 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 446 "   -0.148 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 446 "    0.086 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 446 "   -0.091 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 704 "    0.283 2.00e-02 2.50e+03   1.12e-01 5.04e+02
        pdb=" CG  TRP A 704 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 704 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 704 "   -0.073 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 704 "   -0.096 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 704 "   -0.059 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 704 "   -0.123 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 704 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 704 "   -0.021 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 704 "    0.054 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 704 "    0.079 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 704 "   -0.124 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 704 "   -0.172 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 704 "    0.093 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 704 "    0.028 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 704 "    0.156 2.00e-02 2.50e+03
  ... (remaining 1813 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 861
        2.16 -     2.77: 18837
        2.77 -     3.38: 31982
        3.38 -     3.99: 38674
        3.99 -     4.60: 55478
  Nonbonded interactions: 145832
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 665 "
            pdb=" HG  SER A 779 "
     model   vdw
     1.552 2.450
  nonbonded pdb=" OE1 GLU A 660 "
            pdb=" HG1 THR A 662 "
     model   vdw
     1.584 2.450
  nonbonded pdb=" HG1 THR A 495 "
            pdb=" HA  CYS A 555 "
     model   vdw
     1.601 2.270
  nonbonded pdb=" OD1 ASP A 441 "
            pdb=" HG  SER A 443 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU A  78 "
            pdb=" HG  SER A  82 "
     model   vdw
     1.608 2.450
  ... (remaining 145827 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.440
  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:             0.080
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.840
  Find NCS groups from input model:        0.030
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0070
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      :  0.016   0.072   6184  Z= 0.992
  Angle     :  2.365  17.659   8410  Z= 1.515
  Chirality :  0.133   0.684    868
  Planarity :  0.020   0.147   1117
  Dihedral  : 16.350  82.235   2311
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 1.87
  Ramachandran Plot:
    Outliers :  4.86 %
    Allowed  : 23.52 %
    Favored  : 71.62 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  :  8.35 %
    Favored  : 85.69 %
  Cbeta Deviations :  1.42 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.36 (0.27), residues: 761
  helix: -4.84 (0.38), residues: 14
  sheet: -2.20 (1.15), residues: 24
  loop : -3.27 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 731 
 TYR   0.176   0.024   TYR A 552 
 PHE   0.073   0.014   PHE A 700 
 TRP   0.208   0.041   TRP A 446 
 HIS   0.012   0.004   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.01558 ( 6184)
  covalent geometry    : angle       2.36494 ( 8410)
  hydrogen bonds       : bond        0.14037 (   51)
  hydrogen bonds       : angle      15.84497 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 77
  time to evaluate  : 0.224 
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: 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: 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  201 MET cc_start: -0.0107 (tmm) cc_final: -0.0530 (tpp)
REVERT: A  342 VAL cc_start: -0.2607 (OUTLIER) cc_final: -0.3227 (m)
REVERT: A  632 SER cc_start: 0.0514 (OUTLIER) cc_final: 0.0251 (p)
REVERT: A  728 VAL cc_start: 0.4233 (t) cc_final: 0.3562 (t)
  outliers start: 40
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2239
  time to fit residues: 30.8554
Evaluate side-chains
  65 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue   62 ARG
Chi-restraints excluded: chain A residue  154 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  265 PRO
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  342 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  426 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  547 ASN
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  736 ASN
Chi-restraints excluded: chain A residue  810 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 74 optimal weight:   20.0000
   overall best weight:    8.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  71 GLN
A 212 GLN
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 648 HIS
A 775 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5449 r_free = 0.5449 target = 0.269002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5353 r_free = 0.5353 target = 0.259259 restraints weight = 124817.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5378 r_free = 0.5378 target = 0.261506 restraints weight = 81535.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.5394 r_free = 0.5394 target = 0.263104 restraints weight = 56133.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.5407 r_free = 0.5407 target = 0.264190 restraints weight = 41861.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.5415 r_free = 0.5415 target = 0.264936 restraints weight = 32930.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.5348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0582
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   6184  Z= 0.222
  Angle     :  0.991  11.241   8410  Z= 0.525
  Chirality :  0.055   0.446    868
  Planarity :  0.009   0.106   1117
  Dihedral  : 11.637  57.147    871
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  1.31 %
    Allowed  : 18.66 %
    Favored  : 80.03 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 12.82 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.57 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.38 (0.26), residues: 761
  helix: -4.65 (0.40), residues: 14
  sheet: -2.45 (0.91), residues: 33
  loop : -3.28 (0.21), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 309 
 TYR   0.015   0.002   TYR A 793 
 PHE   0.019   0.002   PHE A  94 
 TRP   0.022   0.003   TRP A 704 
 HIS   0.009   0.002   HIS A 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 6184)
  covalent geometry    : angle       0.99107 ( 8410)
  hydrogen bonds       : bond        0.04664 (   51)
  hydrogen bonds       : angle      13.30259 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 49
  time to evaluate  : 0.226 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.0905 (tmm) cc_final: -0.0264 (mmt)
REVERT: A  445 ARG cc_start: 0.3776 (mtm-85) cc_final: 0.3197 (mtt180)
REVERT: A  482 MET cc_start: -0.2046 (mmt) cc_final: -0.2382 (mmt)
  outliers start: 25
  outliers final: 15
  residues processed: 73
  average time/residue: 0.1654
  time to fit residues: 16.2845
Evaluate side-chains
  58 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 56 optimal weight:   30.0000
   chunk 59 optimal weight:   30.0000
   chunk 30 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 69 optimal weight:    0.7980
   chunk 70 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    4.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 424 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5437 r_free = 0.5437 target = 0.266391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5346 r_free = 0.5346 target = 0.256316 restraints weight = 124210.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5370 r_free = 0.5370 target = 0.258580 restraints weight = 81111.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.5387 r_free = 0.5387 target = 0.260251 restraints weight = 56171.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.261325 restraints weight = 41875.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.5409 r_free = 0.5409 target = 0.262155 restraints weight = 33181.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.5349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0678
moved from start:          0.5987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6184  Z= 0.179
  Angle     :  0.833   8.058   8410  Z= 0.434
  Chirality :  0.053   0.430    868
  Planarity :  0.008   0.103   1117
  Dihedral  :  9.345  56.683    845
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  : 20.50 %
    Favored  : 78.71 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.01 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.03 (0.28), residues: 761
  helix: -4.12 (0.60), residues: 13
  sheet: -2.31 (0.88), residues: 33
  loop : -3.02 (0.22), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 253 
 TYR   0.009   0.002   TYR A 793 
 PHE   0.017   0.002   PHE A  64 
 TRP   0.016   0.002   TRP A 446 
 HIS   0.007   0.001   HIS A 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6184)
  covalent geometry    : angle       0.83336 ( 8410)
  hydrogen bonds       : bond        0.03841 (   51)
  hydrogen bonds       : angle      12.37249 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 43
  time to evaluate  : 0.313 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 MET cc_start: 0.1096 (tmm) cc_final: -0.0052 (mmm)
REVERT: A  793 TYR cc_start: 0.2501 (m-80) cc_final: 0.2288 (m-10)
  outliers start: 23
  outliers final: 17
  residues processed: 63
  average time/residue: 0.1389
  time to fit residues: 12.0102
Evaluate side-chains
  55 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 38
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  294 HIS
Chi-restraints excluded: chain A residue  403 SER
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  482 MET
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:   30.0000
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 44 optimal weight:   50.0000
   chunk 58 optimal weight:   20.0000
   chunk 43 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 74 optimal weight:    5.9990
   chunk 13 optimal weight:   30.0000
   chunk 47 optimal weight:    4.9990
   chunk 54 optimal weight:   20.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 313 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5425 r_free = 0.5425 target = 0.263596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5339 r_free = 0.5339 target = 0.253235 restraints weight = 123049.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5364 r_free = 0.5364 target = 0.255490 restraints weight = 79188.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.5381 r_free = 0.5381 target = 0.257275 restraints weight = 56224.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5390 r_free = 0.5390 target = 0.258364 restraints weight = 41915.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.5398 r_free = 0.5398 target = 0.259101 restraints weight = 33072.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.5334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0879
moved from start:          0.7340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6184  Z= 0.172
  Angle     :  0.769   7.527   8410  Z= 0.401
  Chirality :  0.051   0.416    868
  Planarity :  0.008   0.099   1117
  Dihedral  :  8.575  56.961    844
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 19.32 %
    Favored  : 80.29 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.35 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.88 (0.28), residues: 761
  helix: -4.14 (0.85), residues: 12
  sheet: -2.04 (0.84), residues: 33
  loop : -2.92 (0.22), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 445 
 TYR   0.020   0.002   TYR A 219 
 PHE   0.015   0.002   PHE A  64 
 TRP   0.015   0.002   TRP A 446 
 HIS   0.007   0.001   HIS A 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6184)
  covalent geometry    : angle       0.76932 ( 8410)
  hydrogen bonds       : bond        0.03442 (   51)
  hydrogen bonds       : angle      11.31138 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 37
  time to evaluate  : 0.237 
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: symmetry clash
REVERT: A  115 MET cc_start: -0.0142 (mmp) cc_final: -0.0746 (mmt)
REVERT: A  201 MET cc_start: 0.1500 (tmm) cc_final: 0.0129 (mmt)
REVERT: A  438 PHE cc_start: 0.2175 (OUTLIER) cc_final: 0.1530 (t80)
REVERT: A  658 PHE cc_start: 0.2929 (OUTLIER) cc_final: 0.2299 (t80)
REVERT: A  679 ASP cc_start: 0.5888 (p0) cc_final: 0.5113 (t70)
  outliers start: 21
  outliers final: 14
  residues processed: 57
  average time/residue: 0.1425
  time to fit residues: 10.8199
Evaluate side-chains
  52 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  163 TRP
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  760 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 20 optimal weight:    9.9990
   chunk 44 optimal weight:   20.0000
   chunk 7 optimal weight:   30.0000
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 67 optimal weight:    7.9990
   chunk 24 optimal weight:   30.0000
   chunk 59 optimal weight:   30.0000
   chunk 68 optimal weight:   30.0000
   chunk 70 optimal weight:    6.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 339 ASN
A 533 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5395 r_free = 0.5395 target = 0.258964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.249176 restraints weight = 119248.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.5330 r_free = 0.5330 target = 0.251367 restraints weight = 75636.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5347 r_free = 0.5347 target = 0.252932 restraints weight = 51502.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.5357 r_free = 0.5357 target = 0.253889 restraints weight = 37790.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.5364 r_free = 0.5364 target = 0.254480 restraints weight = 29845.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.5297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1034
moved from start:          0.8818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6184  Z= 0.185
  Angle     :  0.803   8.266   8410  Z= 0.417
  Chirality :  0.052   0.420    868
  Planarity :  0.008   0.090   1117
  Dihedral  :  8.146  58.477    844
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 21.29 %
    Favored  : 78.32 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 14.90 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.83 (0.27), residues: 761
  helix: -3.83 (1.09), residues: 12
  sheet: -1.17 (1.00), residues: 26
  loop : -2.92 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 629 
 TYR   0.020   0.002   TYR A 489 
 PHE   0.018   0.002   PHE A  94 
 TRP   0.013   0.002   TRP A 592 
 HIS   0.008   0.002   HIS A 605 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 6184)
  covalent geometry    : angle       0.80267 ( 8410)
  hydrogen bonds       : bond        0.03444 (   51)
  hydrogen bonds       : angle      11.14638 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.195 
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  115 MET cc_start: 0.0044 (mmp) cc_final: -0.0581 (mmt)
REVERT: A  201 MET cc_start: 0.2118 (tmm) cc_final: 0.0229 (mmm)
REVERT: A  438 PHE cc_start: 0.1813 (OUTLIER) cc_final: 0.1000 (t80)
REVERT: A  658 PHE cc_start: 0.3379 (OUTLIER) cc_final: 0.2824 (t80)
REVERT: A  679 ASP cc_start: 0.6170 (p0) cc_final: 0.5880 (t70)
  outliers start: 24
  outliers final: 17
  residues processed: 57
  average time/residue: 0.1852
  time to fit residues: 13.8145
Evaluate side-chains
  49 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 30
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue   73 CYS
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  324 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 21 optimal weight:   30.0000
   chunk 15 optimal weight:   30.0000
   chunk 56 optimal weight:    8.9990
   chunk 58 optimal weight:   20.0000
   chunk 10 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 42 optimal weight:   10.0000
   chunk 49 optimal weight:   20.0000
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 160 GLN
A 313 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5372 r_free = 0.5372 target = 0.256090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.5292 r_free = 0.5292 target = 0.246311 restraints weight = 119363.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.248532 restraints weight = 75931.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.250093 restraints weight = 52011.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.251042 restraints weight = 38128.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.5347 r_free = 0.5347 target = 0.251629 restraints weight = 30059.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.5272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1078
moved from start:          0.9559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6184  Z= 0.165
  Angle     :  0.741   7.679   8410  Z= 0.381
  Chirality :  0.051   0.419    868
  Planarity :  0.007   0.086   1117
  Dihedral  :  8.067  58.958    844
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  : 20.24 %
    Favored  : 79.24 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 15.95 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.78 (0.28), residues: 761
  helix: -3.95 (1.01), residues: 12
  sheet: -1.20 (0.99), residues: 26
  loop : -2.88 (0.22), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.015   0.001   TYR A 219 
 PHE   0.011   0.001   PHE A  94 
 TRP   0.014   0.002   TRP A 446 
 HIS   0.004   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 6184)
  covalent geometry    : angle       0.74080 ( 8410)
  hydrogen bonds       : bond        0.03278 (   51)
  hydrogen bonds       : angle      10.64905 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 31
  time to evaluate  : 0.301 
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  115 MET cc_start: -0.0144 (mmp) cc_final: -0.0699 (mmt)
REVERT: A  201 MET cc_start: 0.2224 (tmm) cc_final: 0.0566 (tpp)
REVERT: A  438 PHE cc_start: 0.1696 (OUTLIER) cc_final: 0.0964 (t80)
REVERT: A  658 PHE cc_start: 0.3702 (OUTLIER) cc_final: 0.3357 (t80)
REVERT: A  679 ASP cc_start: 0.6217 (p0) cc_final: 0.5878 (t70)
REVERT: A  807 MET cc_start: 0.0779 (mmt) cc_final: 0.0394 (mmp)
  outliers start: 22
  outliers final: 16
  residues processed: 52
  average time/residue: 0.2060
  time to fit residues: 13.6356
Evaluate side-chains
  46 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 28
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 THR
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  254 TRP
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  760 SER
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:   50.0000
   chunk 55 optimal weight:   20.0000
   chunk 45 optimal weight:   40.0000
   chunk 67 optimal weight:   50.0000
   chunk 53 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    8.9990
   chunk 25 optimal weight:    0.5980
   chunk 58 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   overall best weight:    4.0786

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

Flipped N/Q/H residues before XYZ refinement:
A  27 ASN
A  72 GLN
A 313 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5361 r_free = 0.5361 target = 0.255217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.5282 r_free = 0.5282 target = 0.245427 restraints weight = 119738.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.5310 r_free = 0.5310 target = 0.247750 restraints weight = 75481.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.249363 restraints weight = 51834.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.5335 r_free = 0.5335 target = 0.250355 restraints weight = 37939.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.250876 restraints weight = 29599.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.5264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1079
moved from start:          0.9985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6184  Z= 0.129
  Angle     :  0.677   7.602   8410  Z= 0.343
  Chirality :  0.050   0.418    868
  Planarity :  0.007   0.082   1117
  Dihedral  :  7.618  59.456    844
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 18.66 %
    Favored  : 80.95 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 14.90 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.65 (0.28), residues: 761
  helix: -3.76 (1.00), residues: 12
  sheet: -1.29 (0.98), residues: 26
  loop : -2.77 (0.22), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 325 
 TYR   0.012   0.001   TYR A 219 
 PHE   0.008   0.001   PHE A  94 
 TRP   0.011   0.001   TRP A 446 
 HIS   0.005   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6184)
  covalent geometry    : angle       0.67677 ( 8410)
  hydrogen bonds       : bond        0.02913 (   51)
  hydrogen bonds       : angle      10.18834 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 31
  time to evaluate  : 0.252 
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: symmetry clash
   revert: symmetry clash
REVERT: A  115 MET cc_start: -0.0230 (mmp) cc_final: -0.0896 (mmt)
REVERT: A  201 MET cc_start: 0.2216 (tmm) cc_final: 0.0513 (tpp)
REVERT: A  438 PHE cc_start: 0.1556 (OUTLIER) cc_final: 0.0892 (t80)
REVERT: A  680 LYS cc_start: 0.1046 (mttt) cc_final: 0.0510 (pttp)
  outliers start: 21
  outliers final: 17
  residues processed: 51
  average time/residue: 0.2079
  time to fit residues: 13.5505
Evaluate side-chains
  46 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 28
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 PHE
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  658 PHE
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:   50.0000
   chunk 20 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 68 optimal weight:    0.0070
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 44 optimal weight:   30.0000
   chunk 40 optimal weight:   20.0000
   chunk 57 optimal weight:    7.9990
   overall best weight:    5.8006

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 775 GLN
A 810 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5338 r_free = 0.5338 target = 0.252844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5259 r_free = 0.5259 target = 0.242609 restraints weight = 126152.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5285 r_free = 0.5285 target = 0.244890 restraints weight = 80919.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5300 r_free = 0.5300 target = 0.246501 restraints weight = 56208.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.5309 r_free = 0.5309 target = 0.247545 restraints weight = 41621.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.248206 restraints weight = 32602.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.5225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1216
moved from start:          1.0929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6184  Z= 0.151
  Angle     :  0.704   8.248   8410  Z= 0.360
  Chirality :  0.050   0.412    868
  Planarity :  0.007   0.079   1117
  Dihedral  :  7.533  59.846    844
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 20.37 %
    Favored  : 79.24 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.50 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.71 (0.28), residues: 761
  helix: -3.98 (0.88), residues: 17
  sheet: -0.96 (1.01), residues: 26
  loop : -2.82 (0.22), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 331 
 TYR   0.014   0.001   TYR A 283 
 PHE   0.013   0.001   PHE A  94 
 TRP   0.025   0.002   TRP A 254 
 HIS   0.005   0.001   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6184)
  covalent geometry    : angle       0.70427 ( 8410)
  hydrogen bonds       : bond        0.03075 (   51)
  hydrogen bonds       : angle       9.80945 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 35
  time to evaluate  : 0.323 
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  115 MET cc_start: -0.0225 (mmp) cc_final: -0.0955 (mmt)
REVERT: A  201 MET cc_start: 0.2461 (tmm) cc_final: 0.0647 (tpp)
REVERT: A  438 PHE cc_start: 0.1493 (OUTLIER) cc_final: 0.0815 (t80)
  outliers start: 23
  outliers final: 14
  residues processed: 56
  average time/residue: 0.2024
  time to fit residues: 14.2997
Evaluate side-chains
  42 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 27
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  337 THR
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  734 PHE
Chi-restraints excluded: chain A residue  777 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0050
   chunk 24 optimal weight:    0.6980
   chunk 6 optimal weight:   30.0000
   chunk 41 optimal weight:   50.0000
   chunk 17 optimal weight:   30.0000
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 75 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 3 optimal weight:   40.0000
   overall best weight:    2.1400

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
A 322 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 622 HIS
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 775 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5352 r_free = 0.5352 target = 0.253183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5266 r_free = 0.5266 target = 0.242998 restraints weight = 125443.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.5291 r_free = 0.5291 target = 0.245275 restraints weight = 79162.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.246894 restraints weight = 54495.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.5318 r_free = 0.5318 target = 0.247918 restraints weight = 40343.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.5323 r_free = 0.5323 target = 0.248583 restraints weight = 31613.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.5232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1129
moved from start:          1.1097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6184  Z= 0.114
  Angle     :  0.644   7.939   8410  Z= 0.324
  Chirality :  0.049   0.414    868
  Planarity :  0.007   0.076   1117
  Dihedral  :  6.915  52.962    842
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 18.00 %
    Favored  : 81.73 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.69 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.62 (0.28), residues: 761
  helix: -3.84 (0.97), residues: 17
  sheet: -1.93 (0.81), residues: 36
  loop : -2.70 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 325 
 TYR   0.011   0.001   TYR A 219 
 PHE   0.009   0.001   PHE A  94 
 TRP   0.012   0.001   TRP A 334 
 HIS   0.002   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6184)
  covalent geometry    : angle       0.64408 ( 8410)
  hydrogen bonds       : bond        0.02761 (   51)
  hydrogen bonds       : angle       9.49068 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 29
  time to evaluate  : 0.257 
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  115 MET cc_start: -0.0292 (mmp) cc_final: -0.1117 (mmt)
REVERT: A  201 MET cc_start: 0.2320 (tmm) cc_final: 0.0542 (tpp)
REVERT: A  438 PHE cc_start: 0.1502 (OUTLIER) cc_final: 0.0939 (t80)
REVERT: A  680 LYS cc_start: 0.1080 (mttt) cc_final: 0.0767 (pttp)
REVERT: A  807 MET cc_start: -0.0050 (mmt) cc_final: -0.0264 (mmp)
  outliers start: 16
  outliers final: 13
  residues processed: 44
  average time/residue: 0.2074
  time to fit residues: 11.3530
Evaluate side-chains
  42 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 28
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  353 ASP
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  622 HIS
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 14 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 68 optimal weight:    0.1980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 40 optimal weight:   30.0000
   chunk 38 optimal weight:    5.9990
   chunk 5 optimal weight:   40.0000
   chunk 12 optimal weight:   40.0000
   overall best weight:    5.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5345 r_free = 0.5345 target = 0.252234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5257 r_free = 0.5257 target = 0.241903 restraints weight = 126728.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.5281 r_free = 0.5281 target = 0.244149 restraints weight = 80658.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5299 r_free = 0.5299 target = 0.245873 restraints weight = 56019.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.5308 r_free = 0.5308 target = 0.246928 restraints weight = 41054.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.247600 restraints weight = 31928.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.5219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1192
moved from start:          1.1348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6184  Z= 0.131
  Angle     :  0.658   8.147   8410  Z= 0.334
  Chirality :  0.049   0.412    868
  Planarity :  0.007   0.074   1117
  Dihedral  :  6.907  52.510    842
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 20.37 %
    Favored  : 79.37 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 16.69 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.64 (0.28), residues: 761
  helix: -3.74 (1.04), residues: 17
  sheet: -1.98 (0.81), residues: 38
  loop : -2.72 (0.22), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 331 
 TYR   0.012   0.001   TYR A 219 
 PHE   0.007   0.001   PHE A  94 
 TRP   0.013   0.001   TRP A 334 
 HIS   0.003   0.001   HIS A 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6184)
  covalent geometry    : angle       0.65846 ( 8410)
  hydrogen bonds       : bond        0.02957 (   51)
  hydrogen bonds       : angle       9.40278 (   90)

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

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

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1522 Ramachandran restraints generated.
    761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 28
  time to evaluate  : 0.277 
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: symmetry clash
REVERT: A  115 MET cc_start: -0.0321 (mmp) cc_final: -0.1130 (mmt)
REVERT: A  201 MET cc_start: 0.2307 (tmm) cc_final: 0.0500 (tpp)
REVERT: A  438 PHE cc_start: 0.1449 (OUTLIER) cc_final: 0.0897 (t80)
REVERT: A  807 MET cc_start: 0.0074 (mmt) cc_final: -0.0162 (mmp)
  outliers start: 15
  outliers final: 12
  residues processed: 41
  average time/residue: 0.2427
  time to fit residues: 12.1780
Evaluate side-chains
  41 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 28
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 HIS
Chi-restraints excluded: chain A residue  247 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  309 ARG
Chi-restraints excluded: chain A residue  331 ARG
Chi-restraints excluded: chain A residue  353 ASP
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  446 TRP
Chi-restraints excluded: chain A residue  496 THR
Chi-restraints excluded: chain A residue  613 SER
Chi-restraints excluded: chain A residue  625 GLU
Chi-restraints excluded: chain A residue  660 GLU
Chi-restraints excluded: chain A residue  734 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:   30.0000
   chunk 41 optimal weight:   40.0000
   chunk 8 optimal weight:   40.0000
   chunk 67 optimal weight:    9.9990
   chunk 64 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   chunk 9 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0570
   chunk 28 optimal weight:    4.9990
   overall best weight:    3.0106

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 336 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 HIS
A 622 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5347 r_free = 0.5347 target = 0.252085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.5258 r_free = 0.5258 target = 0.241844 restraints weight = 126544.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5287 r_free = 0.5287 target = 0.244163 restraints weight = 81254.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.5303 r_free = 0.5303 target = 0.245796 restraints weight = 55556.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.5313 r_free = 0.5313 target = 0.246818 restraints weight = 40941.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.5319 r_free = 0.5319 target = 0.247492 restraints weight = 32091.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.5225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.1166
moved from start:          1.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6184  Z= 0.117
  Angle     :  0.630   8.522   8410  Z= 0.316
  Chirality :  0.049   0.415    868
  Planarity :  0.007   0.074   1117
  Dihedral  :  6.519  52.387    842
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 17.61 %
    Favored  : 82.13 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 17.14 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.52 (0.28), residues: 761
  helix: -3.80 (0.99), residues: 17
  sheet: -1.76 (0.83), residues: 36
  loop : -2.64 (0.22), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 242 
 TYR   0.012   0.001   TYR A 283 
 PHE   0.004   0.001   PHE A  94 
 TRP   0.015   0.001   TRP A 334 
 HIS   0.012   0.001   HIS A 622 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6184)
  covalent geometry    : angle       0.63018 ( 8410)
  hydrogen bonds       : bond        0.02683 (   51)
  hydrogen bonds       : angle       8.94713 (   90)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2400.59 seconds
wall clock time: 41 minutes 37.62 seconds (2497.62 seconds total)