Starting phenix.real_space_refine
on Fri Oct 10 16:44:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tel_41190/10_2025/8tel_41190.map"
  }
  resolution = 2.77
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      52      5.16       5
     C    5110      2.51       5
     N    1290      2.21       5
     O    1352      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7806
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3903
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3903
          Classifications: {'peptide': 494}
          Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.68, per 1000 atoms: 0.34
  Number of scatterers: 7806
  At special positions: 0
  Unit cell: (85.49, 120.35, 93.79, 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      52     16.00
     P       2     15.00
     O    1352      8.00
     N    1290      7.00
     C    5110      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 416.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1824

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      77.9% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 19
    Processing helix  chain 'A' and resid 21 through 32
      removed outlier: 3.634A  pdb=" N   ALA A  32 " --> pdb=" O   GLY A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 35
      No H-bonds generated for 'chain 'A' and resid 33 through 35'
    Processing helix  chain 'A' and resid 36 through 62
      Proline residue:  A  50  - end of helix
    Processing helix  chain 'A' and resid 67 through 86
    Processing helix  chain 'A' and resid 96 through 112
      removed outlier: 3.686A  pdb=" N   ALA A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 142
    Processing helix  chain 'A' and resid 145 through 151
      removed outlier: 4.184A  pdb=" N   ASN A 149 " --> pdb=" O   CYS A 145 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ARG A 150 " --> pdb=" O   SER A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 178
      removed outlier: 3.792A  pdb=" N   GLY A 156 " --> pdb=" O   THR A 152 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 192
    Processing helix  chain 'A' and resid 193 through 219
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 228 through 251
      removed outlier: 6.415A  pdb=" N   VAL A 240 " --> pdb=" O   ALA A 236 " (cutoff:3.500A)
      Proline residue:  A 241  - end of helix
    Processing helix  chain 'A' and resid 252 through 258
      removed outlier: 4.377A  pdb=" N   GLY A 256 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL A 258 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.731A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 319
      removed outlier: 3.570A  pdb=" N   SER A 313 " --> pdb=" O   TYR A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 325
    Processing helix  chain 'A' and resid 331 through 350
    Processing helix  chain 'A' and resid 359 through 391
      removed outlier: 3.688A  pdb=" N   LYS A 389 " --> pdb=" O   ARG A 385 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR A 390 " --> pdb=" O   ARG A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 409
    Processing helix  chain 'A' and resid 424 through 431
    Processing helix  chain 'A' and resid 442 through 446
    Processing helix  chain 'A' and resid 447 through 453
      removed outlier: 4.291A  pdb=" N   ASP A 453 " --> pdb=" O   GLU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 456
      No H-bonds generated for 'chain 'A' and resid 454 through 456'
    Processing helix  chain 'A' and resid 464 through 477
    Processing helix  chain 'A' and resid 480 through 485
    Processing helix  chain 'A' and resid 488 through 503
      removed outlier: 3.829A  pdb=" N   LEU A 492 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 516
    Processing helix  chain 'B' and resid 8 through 19
    Processing helix  chain 'B' and resid 21 through 32
      removed outlier: 3.634A  pdb=" N   ALA B  32 " --> pdb=" O   GLY B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 35
      No H-bonds generated for 'chain 'B' and resid 33 through 35'
    Processing helix  chain 'B' and resid 36 through 62
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 67 through 86
    Processing helix  chain 'B' and resid 96 through 112
      removed outlier: 3.686A  pdb=" N   ALA B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 142
    Processing helix  chain 'B' and resid 145 through 151
      removed outlier: 4.184A  pdb=" N   ASN B 149 " --> pdb=" O   CYS B 145 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ARG B 150 " --> pdb=" O   SER B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 178
      removed outlier: 3.792A  pdb=" N   GLY B 156 " --> pdb=" O   THR B 152 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   PHE B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 192
    Processing helix  chain 'B' and resid 193 through 219
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 228 through 251
      removed outlier: 6.415A  pdb=" N   VAL B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
    Processing helix  chain 'B' and resid 252 through 258
      removed outlier: 4.377A  pdb=" N   GLY B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   VAL B 258 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.732A  pdb=" N   LEU B 287 " --> pdb=" O   VAL B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 319
      removed outlier: 3.570A  pdb=" N   SER B 313 " --> pdb=" O   TYR B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 325
    Processing helix  chain 'B' and resid 331 through 350
    Processing helix  chain 'B' and resid 359 through 391
      removed outlier: 3.688A  pdb=" N   LYS B 389 " --> pdb=" O   ARG B 385 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   THR B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 409
    Processing helix  chain 'B' and resid 424 through 431
    Processing helix  chain 'B' and resid 442 through 446
    Processing helix  chain 'B' and resid 447 through 453
      removed outlier: 4.292A  pdb=" N   ASP B 453 " --> pdb=" O   GLU B 449 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 456
      No H-bonds generated for 'chain 'B' and resid 454 through 456'
    Processing helix  chain 'B' and resid 464 through 477
    Processing helix  chain 'B' and resid 480 through 485
    Processing helix  chain 'B' and resid 488 through 503
      removed outlier: 3.828A  pdb=" N   LEU B 492 " --> pdb=" O   PRO B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 516
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94
    Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94

    522 hydrogen bonds defined for protein.
    1506 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2420
        1.34 -     1.46: 1850
        1.46 -     1.58: 3630
        1.58 -     1.70: 6
        1.70 -     1.82: 90
  Bond restraints: 7996
  Sorted by residual:
  bond pdb=" OG1 TPO B 410 "
       pdb=" P   TPO B 410 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" OG1 TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.717  1.609  0.108 2.00e-02 2.50e+03 2.91e+01
  bond pdb=" O3P TPO B 410 "
       pdb=" P   TPO B 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O3P TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O2P TPO A 410 "
       pdb=" P   TPO A 410 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.68e+01
  ... (remaining 7991 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 10748
        2.43 -     4.86: 90
        4.86 -     7.29: 4
        7.29 -     9.72: 2
        9.72 -    12.15: 2
  Bond angle restraints: 10846
  Sorted by residual:
  angle pdb=" CB  TPO A 410 "
        pdb=" OG1 TPO A 410 "
        pdb=" P   TPO A 410 "
      ideal   model   delta    sigma   weight residual
     119.31  107.16   12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" CB  TPO B 410 "
        pdb=" OG1 TPO B 410 "
        pdb=" P   TPO B 410 "
      ideal   model   delta    sigma   weight residual
     119.31  107.16   12.15 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" N   VAL B 413 "
        pdb=" CA  VAL B 413 "
        pdb=" C   VAL B 413 "
      ideal   model   delta    sigma   weight residual
     113.53  110.46    3.07 9.80e-01 1.04e+00 9.83e+00
  angle pdb=" N   VAL A 413 "
        pdb=" CA  VAL A 413 "
        pdb=" C   VAL A 413 "
      ideal   model   delta    sigma   weight residual
     113.53  110.48    3.05 9.80e-01 1.04e+00 9.67e+00
  angle pdb=" OG1 TPO B 410 "
        pdb=" P   TPO B 410 "
        pdb=" O1P TPO B 410 "
      ideal   model   delta    sigma   weight residual
     100.43  109.76   -9.33 3.00e+00 1.11e-01 9.66e+00
  ... (remaining 10841 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 4030
       17.68 -    35.37: 506
       35.37 -    53.05: 144
       53.05 -    70.73: 38
       70.73 -    88.42: 10
  Dihedral angle restraints: 4728
    sinusoidal: 1892
      harmonic: 2836
  Sorted by residual:
  dihedral pdb=" CA  ILE B 291 "
           pdb=" C   ILE B 291 "
           pdb=" N   VAL B 292 "
           pdb=" CA  VAL B 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.59   18.41     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ILE A 291 "
           pdb=" C   ILE A 291 "
           pdb=" N   VAL A 292 "
           pdb=" CA  VAL A 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.66   18.34     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CB  GLU B 323 "
           pdb=" CG  GLU B 323 "
           pdb=" CD  GLU B 323 "
           pdb=" OE1 GLU B 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.42   88.42     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 4725 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 863
       0.029 -    0.057: 219
       0.057 -    0.086: 101
       0.086 -    0.114: 38
       0.114 -    0.143: 11
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CA  ILE A 181 "
            pdb=" N   ILE A 181 "
            pdb=" C   ILE A 181 "
            pdb=" CB  ILE A 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.08e-01
  chirality pdb=" CA  ILE B 181 "
            pdb=" N   ILE B 181 "
            pdb=" C   ILE B 181 "
            pdb=" CB  ILE B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  ILE A 262 "
            pdb=" N   ILE A 262 "
            pdb=" C   ILE A 262 "
            pdb=" CB  ILE A 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  ... (remaining 1229 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 258 "   -0.023 5.00e-02 4.00e+02   3.51e-02 1.97e+00
        pdb=" N   PRO B 259 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 259 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 258 "   -0.023 5.00e-02 4.00e+02   3.47e-02 1.93e+00
        pdb=" N   PRO A 259 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 259 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 259 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 226 "    0.009 2.00e-02 2.50e+03   8.01e-03 1.28e+00
        pdb=" CG  TYR A 226 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 226 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 226 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 226 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 226 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 226 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 67
        2.64 -     3.20: 7220
        3.20 -     3.77: 12090
        3.77 -     4.33: 16309
        4.33 -     4.90: 27518
  Nonbonded interactions: 63204
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 298 "
            pdb=" OG  SER A 302 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" O   PHE B 298 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.075 3.040
  nonbonded pdb=" OG  SER A 195 "
            pdb=" OG  SER B 195 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   LYS A 424 "
            pdb=" OG1 THR A 427 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LYS B 424 "
            pdb=" OG1 THR B 427 "
     model   vdw
     2.197 3.040
  ... (remaining 63199 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.360
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108   7996  Z= 0.167
  Angle     :  0.551  12.153  10846  Z= 0.264
  Chirality :  0.035   0.143   1232
  Planarity :  0.003   0.035   1346
  Dihedral  : 17.767  88.419   2904
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 3.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 22.97 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 970
  helix:  2.14 (0.20), residues: 674
  sheet:  None (None), residues: 0
  loop :  0.22 (0.38), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 153 
 TYR   0.019   0.001   TYR A 226 
 PHE   0.004   0.001   PHE A 192 
 TRP   0.005   0.001   TRP A 247 
 HIS   0.002   0.000   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7996)
  covalent geometry    : angle       0.55126 (10846)
  hydrogen bonds       : bond        0.13239 (  522)
  hydrogen bonds       : angle       5.00729 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  226 TYR cc_start: 0.6885 (m-80) cc_final: 0.6522 (m-80)
REVERT: B  226 TYR cc_start: 0.6860 (m-80) cc_final: 0.6517 (m-80)
  outliers start: 10
  outliers final: 10
  residues processed: 95
  average time/residue: 0.5742
  time to fit residues: 57.7484
Evaluate side-chains
  93 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  490 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.3382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.150818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.107194 restraints weight = 8686.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.78
r_work: 0.2972 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7996  Z= 0.149
  Angle     :  0.528   5.505  10846  Z= 0.269
  Chirality :  0.041   0.167   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  5.092  51.236   1076
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 20.33 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.34 (0.26), residues: 970
  helix:  2.20 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.04 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 219 
 TYR   0.015   0.002   TYR A 405 
 PHE   0.009   0.001   PHE B 498 
 TRP   0.008   0.001   TRP B 247 
 HIS   0.005   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7996)
  covalent geometry    : angle       0.52768 (10846)
  hydrogen bonds       : bond        0.05086 (  522)
  hydrogen bonds       : angle       4.11264 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 89
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.7773 (mtt-85) cc_final: 0.6575 (mpt180)
REVERT: A  150 ARG cc_start: 0.7368 (OUTLIER) cc_final: 0.6773 (mpp80)
REVERT: A  181 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6643 (mt)
REVERT: A  242 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8279 (tp)
REVERT: A  385 ARG cc_start: 0.6396 (mtt90) cc_final: 0.5930 (mtm-85)
REVERT: B   20 MET cc_start: 0.8069 (OUTLIER) cc_final: 0.7843 (ptp)
REVERT: B   35 ARG cc_start: 0.7797 (mtt-85) cc_final: 0.6612 (mpt180)
REVERT: B  150 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6773 (mpp80)
REVERT: B  181 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6646 (mt)
REVERT: B  242 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: B  385 ARG cc_start: 0.6447 (mtt90) cc_final: 0.6106 (mtm-85)
  outliers start: 28
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6720
  time to fit residues: 75.5167
Evaluate side-chains
  96 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 40 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A 321 GLN
B  24 GLN
B 321 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.149005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.106194 restraints weight = 8755.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.74
r_work: 0.2947 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7996  Z= 0.217
  Angle     :  0.598   5.930  10846  Z= 0.304
  Chirality :  0.044   0.169   1232
  Planarity :  0.005   0.046   1346
  Dihedral  :  4.744  42.011   1066
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.26 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.26), residues: 970
  helix:  1.77 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop : -0.26 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 197 
 TYR   0.014   0.002   TYR B 405 
 PHE   0.008   0.001   PHE A 324 
 TRP   0.010   0.002   TRP A 247 
 HIS   0.004   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 7996)
  covalent geometry    : angle       0.59765 (10846)
  hydrogen bonds       : bond        0.06405 (  522)
  hydrogen bonds       : angle       4.29733 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 83
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8251 (mtt)
REVERT: A  242 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8295 (tp)
REVERT: A  284 LYS cc_start: 0.7595 (mmtt) cc_final: 0.7051 (mmpt)
REVERT: A  385 ARG cc_start: 0.6486 (mtt90) cc_final: 0.6095 (mtm-85)
REVERT: A  448 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5623 (tp)
REVERT: A  463 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.7497 (pp30)
REVERT: B  135 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8242 (mtt)
REVERT: B  242 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8292 (tp)
REVERT: B  284 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7047 (mmpt)
REVERT: B  385 ARG cc_start: 0.6577 (mtt90) cc_final: 0.6205 (mtm-85)
REVERT: B  448 ILE cc_start: 0.6026 (OUTLIER) cc_final: 0.5610 (tp)
REVERT: B  463 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.7504 (pp30)
  outliers start: 36
  outliers final: 14
  residues processed: 109
  average time/residue: 0.5598
  time to fit residues: 64.7066
Evaluate side-chains
  103 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  173 LYS
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  234 LEU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  228 THR
Chi-restraints excluded: chain B residue  234 LEU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  383 THR
Chi-restraints excluded: chain B residue  388 ILE
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 25 optimal weight:    0.0770
   chunk 4 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 42 optimal weight:    7.9990
   overall best weight:    0.6938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.152785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.110520 restraints weight = 8934.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.75
r_work: 0.2985 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7996  Z= 0.115
  Angle     :  0.469   6.538  10846  Z= 0.239
  Chirality :  0.038   0.156   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  4.224  31.138   1066
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.93 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.30 (0.26), residues: 970
  helix:  2.19 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop : -0.04 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.007   0.001   TYR B  22 
 PHE   0.006   0.001   PHE A 498 
 TRP   0.010   0.001   TRP B 247 
 HIS   0.002   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 7996)
  covalent geometry    : angle       0.46889 (10846)
  hydrogen bonds       : bond        0.04550 (  522)
  hydrogen bonds       : angle       3.97892 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7770 (ptp)
REVERT: A   30 PHE cc_start: 0.7877 (m-80) cc_final: 0.7613 (m-80)
REVERT: A  217 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7111 (mtt90)
REVERT: A  284 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7018 (mmpt)
REVERT: A  385 ARG cc_start: 0.6471 (mtt90) cc_final: 0.6206 (mtm-85)
REVERT: B   30 PHE cc_start: 0.7855 (m-80) cc_final: 0.7568 (m-80)
REVERT: B  217 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7140 (mtt90)
REVERT: B  284 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7027 (mmpt)
REVERT: B  385 ARG cc_start: 0.6518 (mtt90) cc_final: 0.6267 (mtm-85)
  outliers start: 26
  outliers final: 4
  residues processed: 94
  average time/residue: 0.6803
  time to fit residues: 67.2814
Evaluate side-chains
  87 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  390 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    0.0980
   chunk 76 optimal weight:    0.0870
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    0.4980
   chunk 96 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 16 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0470
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.3056

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.156107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.114558 restraints weight = 8944.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.74
r_work: 0.3069 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7996  Z= 0.097
  Angle     :  0.436   6.498  10846  Z= 0.220
  Chirality :  0.037   0.149   1232
  Planarity :  0.004   0.048   1346
  Dihedral  :  3.703  17.936   1064
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 21.53 %
    Favored  : 75.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.68 (0.27), residues: 970
  helix:  2.44 (0.19), residues: 682
  sheet:  None (None), residues: 0
  loop :  0.19 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 232 
 TYR   0.021   0.001   TYR B 405 
 PHE   0.005   0.001   PHE A 498 
 TRP   0.010   0.001   TRP B 247 
 HIS   0.002   0.001   HIS A 406 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 7996)
  covalent geometry    : angle       0.43550 (10846)
  hydrogen bonds       : bond        0.03780 (  522)
  hydrogen bonds       : angle       3.75433 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7641 (ptp)
REVERT: A   30 PHE cc_start: 0.7876 (m-80) cc_final: 0.7613 (m-80)
REVERT: A  217 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7103 (mtt90)
REVERT: A  284 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7033 (mmpt)
REVERT: A  385 ARG cc_start: 0.6468 (mtt90) cc_final: 0.6223 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6708 (m90) cc_final: 0.5894 (t70)
REVERT: A  463 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7285 (pp30)
REVERT: B   20 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7588 (ptp)
REVERT: B  217 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7132 (mtt90)
REVERT: B  284 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7027 (mmpt)
REVERT: B  385 ARG cc_start: 0.6541 (mtt90) cc_final: 0.6296 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6624 (m90) cc_final: 0.5919 (t70)
REVERT: B  463 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.7312 (pp30)
  outliers start: 22
  outliers final: 2
  residues processed: 97
  average time/residue: 0.6201
  time to fit residues: 63.5667
Evaluate side-chains
  91 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 55 optimal weight:    0.0170
   chunk 73 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 88 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.6220

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.154884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112916 restraints weight = 8872.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.74
r_work: 0.3043 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2919 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.103
  Angle     :  0.456   8.669  10846  Z= 0.227
  Chirality :  0.038   0.149   1232
  Planarity :  0.004   0.047   1346
  Dihedral  :  3.668  17.103   1062
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.41 %
    Favored  : 75.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.70 (0.26), residues: 970
  helix:  2.45 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.23 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 232 
 TYR   0.007   0.001   TYR B 495 
 PHE   0.006   0.001   PHE A 498 
 TRP   0.008   0.001   TRP A 247 
 HIS   0.003   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 7996)
  covalent geometry    : angle       0.45641 (10846)
  hydrogen bonds       : bond        0.04105 (  522)
  hydrogen bonds       : angle       3.78495 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 84
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7590 (ptp)
REVERT: A  135 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8279 (mtt)
REVERT: A  217 ARG cc_start: 0.7623 (OUTLIER) cc_final: 0.7061 (mtt90)
REVERT: A  242 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (tp)
REVERT: A  284 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7017 (mmpt)
REVERT: A  385 ARG cc_start: 0.6457 (mtt90) cc_final: 0.6154 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6676 (m90) cc_final: 0.5953 (t70)
REVERT: A  448 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5679 (tp)
REVERT: A  463 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7347 (pp30)
REVERT: B   20 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7554 (ptp)
REVERT: B  135 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8283 (mtt)
REVERT: B  217 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7069 (mtt90)
REVERT: B  242 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8220 (tp)
REVERT: B  284 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7016 (mmpt)
REVERT: B  385 ARG cc_start: 0.6517 (mtt90) cc_final: 0.6212 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6679 (m90) cc_final: 0.5897 (t70)
REVERT: B  448 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5675 (tp)
REVERT: B  463 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.7360 (pp30)
  outliers start: 24
  outliers final: 6
  residues processed: 96
  average time/residue: 0.6204
  time to fit residues: 62.9801
Evaluate side-chains
  100 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 2 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 57 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 85 optimal weight:    2.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.152431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.109968 restraints weight = 8925.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 1.75
r_work: 0.3017 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7996  Z= 0.124
  Angle     :  0.485   6.639  10846  Z= 0.244
  Chirality :  0.039   0.154   1232
  Planarity :  0.004   0.048   1346
  Dihedral  :  3.831  17.196   1062
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 20.93 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.26), residues: 970
  helix:  2.29 (0.19), residues: 680
  sheet:  None (None), residues: 0
  loop :  0.00 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 464 
 TYR   0.021   0.001   TYR B 405 
 PHE   0.006   0.001   PHE A 498 
 TRP   0.008   0.001   TRP B 131 
 HIS   0.003   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7996)
  covalent geometry    : angle       0.48496 (10846)
  hydrogen bonds       : bond        0.04750 (  522)
  hydrogen bonds       : angle       3.90976 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   20 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7664 (ptp)
REVERT: A  135 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8273 (mtt)
REVERT: A  217 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.6848 (mtt90)
REVERT: A  242 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8292 (tp)
REVERT: A  284 LYS cc_start: 0.7535 (mmtt) cc_final: 0.6997 (mmpt)
REVERT: A  385 ARG cc_start: 0.6462 (mtt90) cc_final: 0.6133 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6743 (m90) cc_final: 0.5963 (t70)
REVERT: A  448 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5734 (tp)
REVERT: A  463 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7339 (pp30)
REVERT: B   20 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7642 (ptp)
REVERT: B  135 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8274 (mtt)
REVERT: B  217 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6879 (mtt90)
REVERT: B  242 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8296 (tp)
REVERT: B  284 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7008 (mmpt)
REVERT: B  385 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6182 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6732 (m90) cc_final: 0.5961 (t70)
REVERT: B  448 ILE cc_start: 0.5934 (OUTLIER) cc_final: 0.5713 (tp)
REVERT: B  463 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7360 (pp30)
  outliers start: 26
  outliers final: 6
  residues processed: 93
  average time/residue: 0.6442
  time to fit residues: 63.2962
Evaluate side-chains
  99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 MET
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  217 ARG
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  217 ARG
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 90 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    2.5990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.149272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.106691 restraints weight = 8904.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 1.75
r_work: 0.2948 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   7996  Z= 0.206
  Angle     :  0.582   6.209  10846  Z= 0.297
  Chirality :  0.044   0.167   1232
  Planarity :  0.005   0.049   1346
  Dihedral  :  4.254  17.961   1062
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 22.01 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.26), residues: 970
  helix:  1.85 (0.19), residues: 690
  sheet:  None (None), residues: 0
  loop :  0.30 (0.39), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  60 
 TYR   0.011   0.002   TYR A 495 
 PHE   0.008   0.001   PHE A 179 
 TRP   0.011   0.002   TRP A 230 
 HIS   0.004   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 7996)
  covalent geometry    : angle       0.58152 (10846)
  hydrogen bonds       : bond        0.06088 (  522)
  hydrogen bonds       : angle       4.21170 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8242 (mtt)
REVERT: A  242 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8374 (tp)
REVERT: A  284 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7011 (mmpt)
REVERT: A  292 VAL cc_start: 0.7288 (t) cc_final: 0.7074 (p)
REVERT: A  385 ARG cc_start: 0.6576 (mtt90) cc_final: 0.6253 (mtm-85)
REVERT: A  448 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5744 (tp)
REVERT: A  463 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7492 (pp30)
REVERT: B  135 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8239 (mtt)
REVERT: B  242 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8378 (tp)
REVERT: B  284 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7027 (mmpt)
REVERT: B  292 VAL cc_start: 0.7299 (t) cc_final: 0.7085 (p)
REVERT: B  385 ARG cc_start: 0.6604 (mtt90) cc_final: 0.6199 (mtm-85)
REVERT: B  448 ILE cc_start: 0.6048 (OUTLIER) cc_final: 0.5731 (tp)
REVERT: B  463 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.7497 (pp30)
  outliers start: 22
  outliers final: 6
  residues processed: 94
  average time/residue: 0.6305
  time to fit residues: 62.6236
Evaluate side-chains
  92 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Chi-restraints excluded: chain B residue  499 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9990
   chunk 63 optimal weight:    8.9990
   chunk 67 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 25 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.153015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.111070 restraints weight = 8890.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.74
r_work: 0.3012 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7996  Z= 0.108
  Angle     :  0.463   6.230  10846  Z= 0.234
  Chirality :  0.038   0.151   1232
  Planarity :  0.004   0.050   1346
  Dihedral  :  3.937  17.536   1062
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.61 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.52 (0.27), residues: 970
  helix:  2.25 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.23 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 232 
 TYR   0.020   0.001   TYR B 405 
 PHE   0.006   0.001   PHE A 179 
 TRP   0.011   0.001   TRP B 247 
 HIS   0.002   0.001   HIS A 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 7996)
  covalent geometry    : angle       0.46298 (10846)
  hydrogen bonds       : bond        0.04361 (  522)
  hydrogen bonds       : angle       3.92171 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8270 (mtt)
REVERT: A  150 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6794 (mpp80)
REVERT: A  284 LYS cc_start: 0.7500 (mmtt) cc_final: 0.6982 (mmpt)
REVERT: A  385 ARG cc_start: 0.6541 (mtt90) cc_final: 0.6227 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6808 (m90) cc_final: 0.5989 (t70)
REVERT: A  448 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5809 (tp)
REVERT: A  463 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7365 (pp30)
REVERT: B  135 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8282 (mtt)
REVERT: B  150 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.6832 (mpp80)
REVERT: B  284 LYS cc_start: 0.7507 (mmtt) cc_final: 0.6989 (mmpt)
REVERT: B  385 ARG cc_start: 0.6455 (mtt90) cc_final: 0.6187 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6733 (m90) cc_final: 0.6005 (t70)
REVERT: B  448 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5811 (tp)
REVERT: B  463 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7381 (pp30)
  outliers start: 19
  outliers final: 6
  residues processed: 90
  average time/residue: 0.7191
  time to fit residues: 68.0098
Evaluate side-chains
  90 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 88 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0030
   chunk 13 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 97 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.3594

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.151269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.108908 restraints weight = 8802.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.73
r_work: 0.2984 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7996  Z= 0.137
  Angle     :  0.497   5.858  10846  Z= 0.252
  Chirality :  0.040   0.156   1232
  Planarity :  0.004   0.049   1346
  Dihedral  :  4.013  17.963   1062
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 23.09 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.44 (0.27), residues: 970
  helix:  2.14 (0.19), residues: 696
  sheet:  None (None), residues: 0
  loop :  0.35 (0.39), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  18 
 TYR   0.011   0.001   TYR B 226 
 PHE   0.007   0.001   PHE A  30 
 TRP   0.008   0.001   TRP B 230 
 HIS   0.003   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7996)
  covalent geometry    : angle       0.49650 (10846)
  hydrogen bonds       : bond        0.05024 (  522)
  hydrogen bonds       : angle       4.01990 ( 1506)

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

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

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1940 Ramachandran restraints generated.
    970 Oldfield, 0 Emsley, 970 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  135 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8273 (mtt)
REVERT: A  150 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6793 (mpp80)
REVERT: A  242 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8318 (tp)
REVERT: A  284 LYS cc_start: 0.7499 (mmtt) cc_final: 0.6985 (mmpt)
REVERT: A  385 ARG cc_start: 0.6530 (mtt90) cc_final: 0.6192 (mtm-85)
REVERT: A  406 HIS cc_start: 0.6748 (m90) cc_final: 0.6047 (t70)
REVERT: A  448 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5801 (tp)
REVERT: A  463 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7397 (pp30)
REVERT: B  135 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8277 (mtt)
REVERT: B  150 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6798 (mpp80)
REVERT: B  242 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8319 (tp)
REVERT: B  284 LYS cc_start: 0.7503 (mmtt) cc_final: 0.6987 (mmpt)
REVERT: B  385 ARG cc_start: 0.6469 (mtt90) cc_final: 0.6168 (mtm-85)
REVERT: B  406 HIS cc_start: 0.6759 (m90) cc_final: 0.6059 (t70)
REVERT: B  448 ILE cc_start: 0.6039 (OUTLIER) cc_final: 0.5781 (tp)
REVERT: B  463 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7408 (pp30)
  outliers start: 18
  outliers final: 6
  residues processed: 94
  average time/residue: 0.6589
  time to fit residues: 65.2340
Evaluate side-chains
  95 residues out of total 836 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
Chi-restraints excluded: chain A residue  135 MET
Chi-restraints excluded: chain A residue  150 ARG
Chi-restraints excluded: chain A residue  157 GLU
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  463 GLN
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  150 ARG
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  242 LEU
Chi-restraints excluded: chain B residue  397 LEU
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain B residue  463 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 50 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.8780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.152547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.110482 restraints weight = 8856.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 1.74
r_work: 0.3004 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7996  Z= 0.114
  Angle     :  0.478   8.252  10846  Z= 0.239
  Chirality :  0.038   0.151   1232
  Planarity :  0.004   0.051   1346
  Dihedral  :  3.929  17.490   1062
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.56 %
    Favored  : 74.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.27), residues: 970
  helix:  2.30 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.32 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  18 
 TYR   0.019   0.001   TYR A 405 
 PHE   0.006   0.001   PHE A 498 
 TRP   0.010   0.001   TRP A 247 
 HIS   0.003   0.001   HIS B 312 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 7996)
  covalent geometry    : angle       0.47807 (10846)
  hydrogen bonds       : bond        0.04545 (  522)
  hydrogen bonds       : angle       3.91689 ( 1506)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2846.28 seconds
wall clock time: 49 minutes 15.00 seconds (2955.00 seconds total)