Starting phenix.real_space_refine
on Sat Aug 23 02:23:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qro_18621/08_2025/8qro_18621.map"
  }
  resolution = 2.6
  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=   1.000
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      45      5.16       5
     Na      9      4.78       5
     C    6093      2.51       5
     N    1509      2.21       5
     O    1617      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  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: 9273
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3078
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 414, 3078
          Classifications: {'peptide': 414}
          Link IDs: {'PTRANS': 16, 'TRANS': 397}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 13
          Unusual residues: {' NA': 3}
          Classifications: {'peptide': 1, 'undetermined': 3}
          Modifications used: {'COO': 1}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.00, per 1000 atoms: 0.22
  Number of scatterers: 9273
  At special positions: 0
  Unit cell: (102.828, 101.992, 71.06, 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      45     16.00
     Na      9     11.00
     O    1617      8.00
     N    1509      7.00
     C    6093      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: 1.13
  Conformation dependent library (CDL) restraints added in 376.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2250

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 3 sheets defined
      86.6% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 75
    Processing helix  chain 'A' and resid 77 through 82
    Processing helix  chain 'A' and resid 82 through 90
    Processing helix  chain 'A' and resid 90 through 118
      removed outlier: 3.521A  pdb=" N   GLU A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LEU A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 120 through 154
    Processing helix  chain 'A' and resid 179 through 192
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 230 through 249
    Processing helix  chain 'A' and resid 252 through 291
      removed outlier: 3.889A  pdb=" N   TRP A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   TYR A 276 " --> pdb=" O   TRP A 272 " (cutoff:3.500A)
      Proline residue:  A 278  - end of helix
    Processing helix  chain 'A' and resid 294 through 319
      removed outlier: 3.669A  pdb=" N   LEU A 298 " --> pdb=" O   ASP A 294 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ARG A 301 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LYS A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   TYR A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 329
    Processing helix  chain 'A' and resid 332 through 339
      removed outlier: 3.660A  pdb=" N   PHE A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 351
    Processing helix  chain 'A' and resid 352 through 367
      Proline residue:  A 358  - end of helix
    Processing helix  chain 'A' and resid 371 through 386
      Proline residue:  A 380  - end of helix
      removed outlier: 3.802A  pdb=" N   THR A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 405
    Processing helix  chain 'A' and resid 410 through 428
      removed outlier: 3.921A  pdb=" N   VAL A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY A 427 " --> pdb=" O   ALA A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 446
      removed outlier: 3.853A  pdb=" N   ALA A 440 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 457
      removed outlier: 3.883A  pdb=" N   ILE A 456 " --> pdb=" O   HIS A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 487
      removed outlier: 4.137A  pdb=" N   ARG A 465 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 75
    Processing helix  chain 'B' and resid 77 through 82
    Processing helix  chain 'B' and resid 82 through 90
    Processing helix  chain 'B' and resid 90 through 118
      removed outlier: 3.520A  pdb=" N   GLU B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ILE B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LEU B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
    Processing helix  chain 'B' and resid 120 through 154
    Processing helix  chain 'B' and resid 179 through 192
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 230 through 249
    Processing helix  chain 'B' and resid 252 through 291
      removed outlier: 3.889A  pdb=" N   TRP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR B 276 " --> pdb=" O   TRP B 272 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
    Processing helix  chain 'B' and resid 294 through 319
      removed outlier: 3.669A  pdb=" N   LEU B 298 " --> pdb=" O   ASP B 294 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ARG B 301 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   LYS B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   TYR B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 329
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.660A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
    Processing helix  chain 'B' and resid 352 through 367
      Proline residue:  B 358  - end of helix
    Processing helix  chain 'B' and resid 371 through 386
      Proline residue:  B 380  - end of helix
      removed outlier: 3.803A  pdb=" N   THR B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 405
    Processing helix  chain 'B' and resid 410 through 428
      removed outlier: 3.921A  pdb=" N   VAL B 426 " --> pdb=" O   THR B 422 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY B 427 " --> pdb=" O   ALA B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 446
      removed outlier: 3.854A  pdb=" N   ALA B 440 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   ILE B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 457
      removed outlier: 3.884A  pdb=" N   ILE B 456 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 487
      removed outlier: 4.137A  pdb=" N   ARG B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 75
    Processing helix  chain 'C' and resid 77 through 82
    Processing helix  chain 'C' and resid 82 through 90
    Processing helix  chain 'C' and resid 90 through 118
      removed outlier: 3.520A  pdb=" N   GLU C  94 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE C 103 " --> pdb=" O   LEU C  99 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   LEU C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      Proline residue:  C 106  - end of helix
    Processing helix  chain 'C' and resid 120 through 154
    Processing helix  chain 'C' and resid 179 through 192
    Processing helix  chain 'C' and resid 195 through 200
    Processing helix  chain 'C' and resid 230 through 249
    Processing helix  chain 'C' and resid 252 through 291
      removed outlier: 3.889A  pdb=" N   TRP C 275 " --> pdb=" O   SER C 271 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR C 276 " --> pdb=" O   TRP C 272 " (cutoff:3.500A)
      Proline residue:  C 278  - end of helix
    Processing helix  chain 'C' and resid 294 through 319
      removed outlier: 3.669A  pdb=" N   LEU C 298 " --> pdb=" O   ASP C 294 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ARG C 301 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
      removed outlier: 7.252A  pdb=" N   LYS C 304 " --> pdb=" O   ALA C 300 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   TYR C 305 " --> pdb=" O   ARG C 301 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 319 through 329
    Processing helix  chain 'C' and resid 332 through 339
      removed outlier: 3.660A  pdb=" N   PHE C 336 " --> pdb=" O   ASN C 332 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 340 through 351
    Processing helix  chain 'C' and resid 352 through 367
      Proline residue:  C 358  - end of helix
    Processing helix  chain 'C' and resid 371 through 386
      Proline residue:  C 380  - end of helix
      removed outlier: 3.803A  pdb=" N   THR C 384 " --> pdb=" O   PRO C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 405
    Processing helix  chain 'C' and resid 410 through 428
      removed outlier: 3.921A  pdb=" N   VAL C 426 " --> pdb=" O   THR C 422 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY C 427 " --> pdb=" O   ALA C 423 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 435 through 446
      removed outlier: 3.853A  pdb=" N   ALA C 440 " --> pdb=" O   VAL C 436 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   ILE C 441 " --> pdb=" O   LEU C 437 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 457
      removed outlier: 3.884A  pdb=" N   ILE C 456 " --> pdb=" O   HIS C 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 459 through 487
      removed outlier: 4.137A  pdb=" N   ARG C 465 " --> pdb=" O   TRP C 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 209
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 209
    Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 209

    775 hydrogen bonds defined for protein.
    2316 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: 1.45

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2928
        1.34 -     1.46: 1858
        1.46 -     1.58: 4571
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9429
  Sorted by residual:
  bond pdb=" N   LEU B  49 "
       pdb=" CA  LEU B  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   LEU A  49 "
       pdb=" CA  LEU A  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
  bond pdb=" N   LEU C  49 "
       pdb=" CA  LEU C  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   GLN A 604 "
       pdb=" CA  GLN A 604 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" N   GLN B 604 "
       pdb=" CA  GLN B 604 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.87e+00
  ... (remaining 9424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.89: 12055
        0.89 -     1.78: 604
        1.78 -     2.67: 104
        2.67 -     3.56: 47
        3.56 -     4.44: 33
  Bond angle restraints: 12843
  Sorted by residual:
  angle pdb=" CA  PHE A 299 "
        pdb=" C   PHE A 299 "
        pdb=" O   PHE A 299 "
      ideal   model   delta    sigma   weight residual
     120.70  118.49    2.21 1.03e+00 9.43e-01 4.59e+00
  angle pdb=" CA  PHE B 299 "
        pdb=" C   PHE B 299 "
        pdb=" O   PHE B 299 "
      ideal   model   delta    sigma   weight residual
     120.70  118.52    2.18 1.03e+00 9.43e-01 4.46e+00
  angle pdb=" CA  PHE C 299 "
        pdb=" C   PHE C 299 "
        pdb=" O   PHE C 299 "
      ideal   model   delta    sigma   weight residual
     120.70  118.54    2.16 1.03e+00 9.43e-01 4.41e+00
  angle pdb=" N   VAL C  90 "
        pdb=" CA  VAL C  90 "
        pdb=" C   VAL C  90 "
      ideal   model   delta    sigma   weight residual
     109.34  113.24   -3.90 2.08e+00 2.31e-01 3.52e+00
  angle pdb=" N   PHE B 299 "
        pdb=" CA  PHE B 299 "
        pdb=" C   PHE B 299 "
      ideal   model   delta    sigma   weight residual
     111.14  113.16   -2.02 1.08e+00 8.57e-01 3.50e+00
  ... (remaining 12838 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.48: 4821
       12.48 -    24.97: 525
       24.97 -    37.45: 126
       37.45 -    49.94: 39
       49.94 -    62.42: 15
  Dihedral angle restraints: 5526
    sinusoidal: 2022
      harmonic: 3504
  Sorted by residual:
  dihedral pdb=" CA  LEU C 455 "
           pdb=" CB  LEU C 455 "
           pdb=" CG  LEU C 455 "
           pdb=" CD1 LEU C 455 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.43  -54.43     3      1.50e+01 4.44e-03 9.28e+00
  dihedral pdb=" CA  LEU A 455 "
           pdb=" CB  LEU A 455 "
           pdb=" CG  LEU A 455 "
           pdb=" CD1 LEU A 455 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.42  -54.42     3      1.50e+01 4.44e-03 9.28e+00
  dihedral pdb=" CA  LEU B 455 "
           pdb=" CB  LEU B 455 "
           pdb=" CG  LEU B 455 "
           pdb=" CD1 LEU B 455 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  114.40  -54.40     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 5523 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 1092
       0.026 -    0.053: 232
       0.053 -    0.079: 189
       0.079 -    0.105: 69
       0.105 -    0.131: 29
  Chirality restraints: 1611
  Sorted by residual:
  chirality pdb=" CB  ILE B 289 "
            pdb=" CA  ILE B 289 "
            pdb=" CG1 ILE B 289 "
            pdb=" CG2 ILE B 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  VAL B 220 "
            pdb=" N   VAL B 220 "
            pdb=" C   VAL B 220 "
            pdb=" CB  VAL B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CB  ILE C 289 "
            pdb=" CA  ILE C 289 "
            pdb=" CG1 ILE C 289 "
            pdb=" CG2 ILE C 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1608 not shown)

  Planarity restraints: 1587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 357 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO A 358 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 358 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 358 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 357 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO C 358 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C 358 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 358 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 357 "   -0.026 5.00e-02 4.00e+02   4.01e-02 2.58e+00
        pdb=" N   PRO B 358 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 358 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 358 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1584 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1734
        2.76 -     3.30: 9812
        3.30 -     3.83: 16750
        3.83 -     4.37: 19125
        4.37 -     4.90: 33800
  Nonbonded interactions: 81221
  Sorted by model distance:
  nonbonded pdb=" CD1 PHE A 393 "
            pdb=" CG1 VAL A 463 "
     model   vdw
     2.231 3.760
  nonbonded pdb=" CD1 PHE B 393 "
            pdb=" CG1 VAL B 463 "
     model   vdw
     2.231 3.760
  nonbonded pdb=" CD1 PHE C 393 "
            pdb=" CG1 VAL C 463 "
     model   vdw
     2.231 3.760
  nonbonded pdb=" OG1 THR B 138 "
            pdb="NA    NA B 603 "
     model   vdw
     2.241 2.470
  nonbonded pdb=" OG1 THR A 138 "
            pdb="NA    NA A 603 "
     model   vdw
     2.241 2.470
  ... (remaining 81216 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.060
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.010
  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:6.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
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      :  0.002   0.033   9429  Z= 0.126
  Angle     :  0.519   4.445  12843  Z= 0.291
  Chirality :  0.037   0.131   1611
  Planarity :  0.004   0.040   1587
  Dihedral  : 11.990  62.424   3276
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  7.34 %
    Favored  : 92.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.95 (0.24), residues: 1224
  helix:  1.19 (0.16), residues: 981
  sheet: -1.43 (0.65), residues: 60
  loop : -1.37 (0.38), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 330 
 TYR   0.007   0.001   TYR A 208 
 PHE   0.009   0.001   PHE A 299 
 TRP   0.006   0.001   TRP A 275 
 HIS   0.001   0.001   HIS C 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 9429)
  covalent geometry    : angle       0.51869 (12843)
  hydrogen bonds       : bond        0.11097 (  775)
  hydrogen bonds       : angle       5.38920 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  224 GLN cc_start: 0.8159 (pm20) cc_final: 0.7761 (pm20)
REVERT: A  400 PHE cc_start: 0.7795 (t80) cc_final: 0.7498 (t80)
REVERT: B  400 PHE cc_start: 0.7759 (t80) cc_final: 0.7497 (t80)
REVERT: C  224 GLN cc_start: 0.8192 (pm20) cc_final: 0.7897 (pm20)
REVERT: C  274 MET cc_start: 0.8267 (mtm) cc_final: 0.7965 (mtt)
REVERT: C  387 MET cc_start: 0.8842 (mtt) cc_final: 0.8622 (mtt)
REVERT: C  400 PHE cc_start: 0.7650 (t80) cc_final: 0.7422 (t80)
REVERT: C  475 ASP cc_start: 0.7561 (m-30) cc_final: 0.7205 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 128
  average time/residue: 0.4550
  time to fit residues: 62.7542
Evaluate side-chains
  105 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    6.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
A 452 HIS
B 367 ASN
B 484 ASN
C 367 ASN
C 452 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.146899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.094095 restraints weight = 10645.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 2.03
r_work: 0.2917 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9429  Z= 0.160
  Angle     :  0.549   5.651  12843  Z= 0.276
  Chirality :  0.040   0.142   1611
  Planarity :  0.005   0.041   1587
  Dihedral  :  3.549  12.588   1302
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  :  9.48 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.93 (0.24), residues: 1224
  helix:  1.76 (0.16), residues: 1026
  sheet:  None (None), residues: 0
  loop : -1.19 (0.37), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 376 
 TYR   0.010   0.001   TYR B 208 
 PHE   0.013   0.002   PHE C 237 
 TRP   0.006   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 9429)
  covalent geometry    : angle       0.54867 (12843)
  hydrogen bonds       : bond        0.04512 (  775)
  hydrogen bonds       : angle       4.71924 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5861 (mtp85)
REVERT: A  179 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7102 (mm-30)
REVERT: A  452 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6911 (m-70)
REVERT: B   85 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.5483 (mtp85)
REVERT: B  291 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7351 (mt-10)
REVERT: C   85 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5750 (mtp85)
REVERT: C  274 MET cc_start: 0.8339 (mtm) cc_final: 0.8015 (mtt)
REVERT: C  328 PHE cc_start: 0.8608 (m-80) cc_final: 0.8366 (m-80)
REVERT: C  475 ASP cc_start: 0.6885 (m-30) cc_final: 0.6566 (m-30)
  outliers start: 21
  outliers final: 3
  residues processed: 130
  average time/residue: 0.5175
  time to fit residues: 72.0212
Evaluate side-chains
  108 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  452 HIS
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 120 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 90 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9990
   overall best weight:    0.6742

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN
A 452 HIS
B 484 ASN
C 367 ASN
C 484 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.148575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.095980 restraints weight = 10643.645|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.03
r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9429  Z= 0.119
  Angle     :  0.497   5.488  12843  Z= 0.249
  Chirality :  0.038   0.133   1611
  Planarity :  0.005   0.044   1587
  Dihedral  :  3.441  12.392   1302
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 11.72 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.46 (0.24), residues: 1224
  helix:  2.11 (0.16), residues: 1020
  sheet:  None (None), residues: 0
  loop : -0.85 (0.38), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 465 
 TYR   0.009   0.001   TYR B 208 
 PHE   0.011   0.001   PHE A 400 
 TRP   0.005   0.001   TRP A 275 
 HIS   0.012   0.001   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9429)
  covalent geometry    : angle       0.49653 (12843)
  hydrogen bonds       : bond        0.03954 (  775)
  hydrogen bonds       : angle       4.49999 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5837 (mtp85)
REVERT: A  179 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7052 (mm-30)
REVERT: B   85 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5352 (mtp85)
REVERT: B  291 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7334 (mt-10)
REVERT: B  330 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6622 (mpt180)
REVERT: C   85 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5749 (mtp85)
REVERT: C  179 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7189 (mm-30)
REVERT: C  274 MET cc_start: 0.8280 (mtm) cc_final: 0.7970 (mtt)
REVERT: C  330 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6589 (mpt180)
REVERT: C  367 ASN cc_start: 0.8464 (m-40) cc_final: 0.8188 (m110)
REVERT: C  388 ASP cc_start: 0.7934 (OUTLIER) cc_final: 0.7380 (m-30)
REVERT: C  475 ASP cc_start: 0.6782 (m-30) cc_final: 0.6466 (m-30)
  outliers start: 19
  outliers final: 3
  residues processed: 117
  average time/residue: 0.4907
  time to fit residues: 61.3096
Evaluate side-chains
  109 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  388 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 44 optimal weight:    8.9990
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0980
   chunk 13 optimal weight:    0.5980
   chunk 108 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 106 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
B 484 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.147912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.095317 restraints weight = 10708.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.02
r_work: 0.2943 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9429  Z= 0.124
  Angle     :  0.490   7.062  12843  Z= 0.244
  Chirality :  0.038   0.137   1611
  Planarity :  0.005   0.044   1587
  Dihedral  :  3.418  13.003   1302
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 12.03 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.69 (0.24), residues: 1224
  helix:  2.23 (0.16), residues: 1017
  sheet:  None (None), residues: 0
  loop : -0.50 (0.42), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 376 
 TYR   0.008   0.001   TYR B 208 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.006   0.001   TRP A 130 
 HIS   0.001   0.000   HIS A 452 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9429)
  covalent geometry    : angle       0.48968 (12843)
  hydrogen bonds       : bond        0.03920 (  775)
  hydrogen bonds       : angle       4.43471 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.5889 (mtp85)
REVERT: A  179 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7018 (mm-30)
REVERT: B   85 ARG cc_start: 0.6211 (OUTLIER) cc_final: 0.5363 (mtp85)
REVERT: B  291 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7359 (mt-10)
REVERT: B  330 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6796 (mpt180)
REVERT: C   85 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5789 (mtp85)
REVERT: C  179 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7269 (mm-30)
REVERT: C  274 MET cc_start: 0.8298 (mtm) cc_final: 0.8002 (mtt)
REVERT: C  330 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6613 (mpt180)
REVERT: C  367 ASN cc_start: 0.8469 (m-40) cc_final: 0.8192 (m110)
REVERT: C  388 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7277 (m-30)
REVERT: C  475 ASP cc_start: 0.6752 (m-30) cc_final: 0.6444 (m-30)
  outliers start: 19
  outliers final: 5
  residues processed: 122
  average time/residue: 0.5059
  time to fit residues: 65.9634
Evaluate side-chains
  118 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  388 ASP
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 120 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.144705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.091378 restraints weight = 10638.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.00
r_work: 0.2886 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9429  Z= 0.193
  Angle     :  0.538   6.795  12843  Z= 0.269
  Chirality :  0.040   0.144   1611
  Planarity :  0.005   0.042   1587
  Dihedral  :  3.552  12.751   1302
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 11.72 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.37 (0.24), residues: 1224
  helix:  1.95 (0.16), residues: 1023
  sheet:  None (None), residues: 0
  loop : -0.34 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 376 
 TYR   0.014   0.002   TYR C 334 
 PHE   0.015   0.002   PHE C 237 
 TRP   0.007   0.001   TRP A 130 
 HIS   0.002   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 9429)
  covalent geometry    : angle       0.53756 (12843)
  hydrogen bonds       : bond        0.04566 (  775)
  hydrogen bonds       : angle       4.60396 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6332 (OUTLIER) cc_final: 0.5925 (mtp85)
REVERT: A  179 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7147 (mm-30)
REVERT: A  247 LYS cc_start: 0.8364 (mmtt) cc_final: 0.7882 (mtpt)
REVERT: B   85 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.5453 (mtp85)
REVERT: B  291 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: B  330 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6747 (mpt180)
REVERT: C   85 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.5792 (mtp85)
REVERT: C  179 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7294 (mm-30)
REVERT: C  330 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6615 (mpt180)
REVERT: C  367 ASN cc_start: 0.8479 (m-40) cc_final: 0.8220 (m110)
REVERT: C  475 ASP cc_start: 0.6855 (m-30) cc_final: 0.6554 (m-30)
  outliers start: 28
  outliers final: 11
  residues processed: 135
  average time/residue: 0.5300
  time to fit residues: 76.8725
Evaluate side-chains
  123 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  330 ARG
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  330 ARG
Chi-restraints excluded: chain C residue  393 PHE
Chi-restraints excluded: chain C residue  466 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 97 optimal weight:    2.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN
B 367 ASN
B 484 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.146741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.094196 restraints weight = 10677.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3086 rms_B_bonded: 1.96
r_work: 0.2926 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2780 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9429  Z= 0.132
  Angle     :  0.494   6.205  12843  Z= 0.248
  Chirality :  0.038   0.137   1611
  Planarity :  0.005   0.045   1587
  Dihedral  :  3.476  12.936   1302
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 12.64 %
    Favored  : 84.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.63 (0.24), residues: 1224
  helix:  2.16 (0.16), residues: 1017
  sheet:  None (None), residues: 0
  loop : -0.36 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 376 
 TYR   0.008   0.001   TYR A 334 
 PHE   0.012   0.001   PHE B 237 
 TRP   0.008   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9429)
  covalent geometry    : angle       0.49360 (12843)
  hydrogen bonds       : bond        0.04046 (  775)
  hydrogen bonds       : angle       4.49491 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5974 (mtp85)
REVERT: A  179 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7168 (mm-30)
REVERT: B   85 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5431 (mtp85)
REVERT: B  291 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7410 (mt-10)
REVERT: C   85 ARG cc_start: 0.6452 (OUTLIER) cc_final: 0.5823 (mtp85)
REVERT: C  179 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7299 (mm-30)
REVERT: C  367 ASN cc_start: 0.8470 (m-40) cc_final: 0.8221 (m110)
REVERT: C  475 ASP cc_start: 0.6853 (m-30) cc_final: 0.6574 (m-30)
  outliers start: 25
  outliers final: 9
  residues processed: 131
  average time/residue: 0.5536
  time to fit residues: 77.7416
Evaluate side-chains
  121 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue  274 MET
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  384 THR
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 109 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.147703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.094974 restraints weight = 10693.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.00
r_work: 0.2942 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9429  Z= 0.123
  Angle     :  0.484   6.087  12843  Z= 0.241
  Chirality :  0.037   0.136   1611
  Planarity :  0.005   0.047   1587
  Dihedral  :  3.398  12.092   1302
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.56 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.81 (0.24), residues: 1224
  helix:  2.23 (0.16), residues: 1035
  sheet:  None (None), residues: 0
  loop : -0.18 (0.45), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 376 
 TYR   0.007   0.001   TYR B 334 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.010   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 9429)
  covalent geometry    : angle       0.48419 (12843)
  hydrogen bonds       : bond        0.03873 (  775)
  hydrogen bonds       : angle       4.39925 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6255 (OUTLIER) cc_final: 0.5891 (mtp85)
REVERT: A  179 GLU cc_start: 0.7491 (mm-30) cc_final: 0.7082 (mm-30)
REVERT: A  366 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7082 (mm-30)
REVERT: B   85 ARG cc_start: 0.6182 (OUTLIER) cc_final: 0.5342 (mtp85)
REVERT: B  291 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7383 (mt-10)
REVERT: C   85 ARG cc_start: 0.6387 (OUTLIER) cc_final: 0.5743 (mtp85)
REVERT: C  179 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7293 (mm-30)
REVERT: C  367 ASN cc_start: 0.8390 (m-40) cc_final: 0.8131 (m110)
REVERT: C  475 ASP cc_start: 0.6765 (m-30) cc_final: 0.6486 (m-30)
  outliers start: 19
  outliers final: 10
  residues processed: 131
  average time/residue: 0.5252
  time to fit residues: 74.1652
Evaluate side-chains
  124 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LEU
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  384 THR
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 35 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0980
   chunk 73 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN
B 367 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.147926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.095274 restraints weight = 10580.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 2.02
r_work: 0.2945 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9429  Z= 0.119
  Angle     :  0.489   6.693  12843  Z= 0.241
  Chirality :  0.037   0.135   1611
  Planarity :  0.005   0.048   1587
  Dihedral  :  3.400  13.380   1302
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.97 %
    Favored  : 84.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.87 (0.24), residues: 1224
  helix:  2.34 (0.16), residues: 1017
  sheet:  None (None), residues: 0
  loop : -0.34 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 376 
 TYR   0.007   0.001   TYR B 334 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.010   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9429)
  covalent geometry    : angle       0.48855 (12843)
  hydrogen bonds       : bond        0.03803 (  775)
  hydrogen bonds       : angle       4.35054 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.5834 (mtp85)
REVERT: A  179 GLU cc_start: 0.7391 (mm-30) cc_final: 0.6992 (mm-30)
REVERT: A  366 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7096 (mm-30)
REVERT: B   85 ARG cc_start: 0.6103 (OUTLIER) cc_final: 0.5264 (mtp85)
REVERT: B  291 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7339 (mt-10)
REVERT: C   85 ARG cc_start: 0.6310 (OUTLIER) cc_final: 0.5666 (mtp85)
REVERT: C  179 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7244 (mm-30)
REVERT: C  367 ASN cc_start: 0.8326 (m-40) cc_final: 0.8066 (m110)
REVERT: C  475 ASP cc_start: 0.6679 (m-30) cc_final: 0.6393 (m-30)
  outliers start: 20
  outliers final: 10
  residues processed: 130
  average time/residue: 0.5212
  time to fit residues: 73.2497
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  384 THR
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 61 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0980
   chunk 69 optimal weight:    7.9990
   chunk 102 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 100 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
C 484 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.095986 restraints weight = 10594.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.99
r_work: 0.2956 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9429  Z= 0.116
  Angle     :  0.486   6.305  12843  Z= 0.239
  Chirality :  0.037   0.135   1611
  Planarity :  0.005   0.048   1587
  Dihedral  :  3.382  14.168   1302
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.68 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.93 (0.24), residues: 1224
  helix:  2.38 (0.16), residues: 1017
  sheet:  None (None), residues: 0
  loop : -0.35 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 202 
 TYR   0.007   0.001   TYR C 208 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.010   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 9429)
  covalent geometry    : angle       0.48630 (12843)
  hydrogen bonds       : bond        0.03767 (  775)
  hydrogen bonds       : angle       4.32025 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5790 (mtp85)
REVERT: A  366 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7202 (mm-30)
REVERT: B   85 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5350 (mtp85)
REVERT: B  291 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7372 (mt-10)
REVERT: B  366 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7095 (mm-30)
REVERT: C   85 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5693 (mtp85)
REVERT: C  366 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7165 (mm-30)
REVERT: C  367 ASN cc_start: 0.8365 (m-40) cc_final: 0.8125 (m110)
REVERT: C  475 ASP cc_start: 0.6718 (m-30) cc_final: 0.6429 (m-30)
  outliers start: 18
  outliers final: 9
  residues processed: 134
  average time/residue: 0.5293
  time to fit residues: 76.5149
Evaluate side-chains
  128 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain B residue   85 ARG
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  384 THR
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 224 GLN
A 367 ASN
B 367 ASN
C 484 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.148397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096016 restraints weight = 10566.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 1.96
r_work: 0.2957 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2811 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9429  Z= 0.120
  Angle     :  0.497   7.137  12843  Z= 0.243
  Chirality :  0.037   0.138   1611
  Planarity :  0.005   0.049   1587
  Dihedral  :  3.377  14.423   1302
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 15.09 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.96 (0.24), residues: 1224
  helix:  2.39 (0.16), residues: 1017
  sheet: -1.51 (0.67), residues: 60
  loop :  0.48 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 376 
 TYR   0.009   0.001   TYR C 208 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.010   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 9429)
  covalent geometry    : angle       0.49683 (12843)
  hydrogen bonds       : bond        0.03800 (  775)
  hydrogen bonds       : angle       4.31660 ( 2316)

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

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

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2448 Ramachandran restraints generated.
    1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A   85 ARG cc_start: 0.6200 (OUTLIER) cc_final: 0.5863 (mtp85)
REVERT: A  366 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7213 (mm-30)
REVERT: B  291 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7401 (mt-10)
REVERT: B  366 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7118 (mm-30)
REVERT: C   85 ARG cc_start: 0.6427 (OUTLIER) cc_final: 0.5739 (mtp85)
REVERT: C  366 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7214 (mm-30)
REVERT: C  367 ASN cc_start: 0.8409 (m-40) cc_final: 0.8169 (m110)
REVERT: C  475 ASP cc_start: 0.6795 (m-30) cc_final: 0.6510 (m-30)
  outliers start: 15
  outliers final: 10
  residues processed: 129
  average time/residue: 0.5370
  time to fit residues: 74.5426
Evaluate side-chains
  127 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ARG
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  308 CYS
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   85 ARG
Chi-restraints excluded: chain C residue  384 THR
Chi-restraints excluded: chain C residue  393 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.4980
   chunk 15 optimal weight:    0.1980
   chunk 48 optimal weight:    0.9980
   chunk 103 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0060
   chunk 106 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 367 ASN
B 367 ASN
C 484 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.096033 restraints weight = 10492.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.95
r_work: 0.2958 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.242   9429  Z= 0.213
  Angle     :  0.914  59.200  12843  Z= 0.512
  Chirality :  0.039   0.505   1611
  Planarity :  0.005   0.049   1587
  Dihedral  :  3.374  14.408   1302
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 15.49 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.96 (0.24), residues: 1224
  helix:  2.39 (0.16), residues: 1017
  sheet: -1.56 (0.67), residues: 60
  loop :  0.47 (0.53), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 376 
 TYR   0.009   0.001   TYR C 208 
 PHE   0.011   0.001   PHE B 237 
 TRP   0.009   0.001   TRP A 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 9429)
  covalent geometry    : angle       0.91445 (12843)
  hydrogen bonds       : bond        0.03793 (  775)
  hydrogen bonds       : angle       4.32026 ( 2316)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3480.32 seconds
wall clock time: 60 minutes 3.56 seconds (3603.56 seconds total)