Starting phenix.real_space_refine
on Tue Mar  3 23:49:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvb_4646/03_2026/6qvb_4646.cif"
  }
  resolution = 4.34
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    6109      2.51       5
     N    1482      2.21       5
     O    1576      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9237
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4617
          Classifications: {'peptide': 596}
          Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 566}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 4620
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4620
          Classifications: {'peptide': 597}
          Link IDs: {'CIS': 2, 'PTRANS': 27, 'TRANS': 567}
          Chain breaks: 3
  Time building chain proxies: 2.31, per 1000 atoms: 0.25
  Number of scatterers: 9237
  At special positions: 0
  Unit cell: (110.21, 118.77, 108.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    1576      8.00
     N    1482      7.00
     C    6109      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: 0.67
  Conformation dependent library (CDL) restraints added in 332.4 milliseconds
  

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2202

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 6 sheets defined
      66.6% alpha, 3.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 115 through 153
    Processing helix  chain 'B' and resid 158 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.499A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 209 through 224
      removed outlier: 4.283A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B 214 " --> pdb=" O   LYS B 210 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 323
      removed outlier: 3.778A  pdb=" N   TYR B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   VAL B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 375
      removed outlier: 3.717A  pdb=" N   ALA B 352 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   CYS B 357 " --> pdb=" O   ALA B 353 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY B 359 " --> pdb=" O   GLY B 355 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 388
    Processing helix  chain 'B' and resid 389 through 393
      removed outlier: 3.546A  pdb=" N   LEU B 392 " --> pdb=" O   HIS B 389 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR B 393 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 389 through 393'
    Processing helix  chain 'B' and resid 394 through 404
      removed outlier: 3.520A  pdb=" N   THR B 398 " --> pdb=" O   PRO B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 415
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 444 through 450
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 4.867A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 538
      removed outlier: 4.613A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.881A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 585
      removed outlier: 3.723A  pdb=" N   SER B 580 " --> pdb=" O   SER B 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 632
      removed outlier: 4.074A  pdb=" N   THR B 632 " --> pdb=" O   LEU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 666
    Processing helix  chain 'B' and resid 833 through 845
    Processing helix  chain 'B' and resid 863 through 872
      removed outlier: 3.947A  pdb=" N   GLY B 872 " --> pdb=" O   LYS B 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 153
    Processing helix  chain 'A' and resid 158 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 4.492A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 209 through 224
      removed outlier: 4.269A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 323
      removed outlier: 3.872A  pdb=" N   TYR A 302 " --> pdb=" O   ALA A 298 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 375
      removed outlier: 3.692A  pdb=" N   ALA A 352 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS A 357 " --> pdb=" O   ALA A 353 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY A 359 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 389 through 393
      removed outlier: 3.549A  pdb=" N   LEU A 392 " --> pdb=" O   HIS A 389 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   TYR A 393 " --> pdb=" O   ARG A 390 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 389 through 393'
    Processing helix  chain 'A' and resid 394 through 404
      removed outlier: 3.670A  pdb=" N   THR A 398 " --> pdb=" O   PRO A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 444 through 450
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 4.763A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 4.738A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 4.060A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
    Processing helix  chain 'A' and resid 576 through 585
      removed outlier: 3.696A  pdb=" N   SER A 580 " --> pdb=" O   SER A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 632
      removed outlier: 4.082A  pdb=" N   THR A 632 " --> pdb=" O   LEU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 666
    Processing helix  chain 'A' and resid 833 through 845
    Processing helix  chain 'A' and resid 862 through 872
      removed outlier: 3.830A  pdb=" N   LEU A 866 " --> pdb=" O   ALA A 862 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLY A 872 " --> pdb=" O   LYS A 868 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'B' and resid 636 through 640
      removed outlier: 6.078A  pdb=" N   LEU B 637 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   SER B 651 " --> pdb=" O   LEU B 637 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU B 639 " --> pdb=" O   LEU B 649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 5.978A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   VAL B 851 " --> pdb=" O   ARG B 858 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'A' and resid 636 through 640
      removed outlier: 6.020A  pdb=" N   LEU A 637 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER A 651 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU A 639 " --> pdb=" O   LEU A 649 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 5.979A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    561 hydrogen bonds defined for protein.
    1629 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: 1.47

  Time building geometry restraints manager: 0.93 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: 2735
        1.34 -     1.46: 2230
        1.46 -     1.58: 4384
        1.58 -     1.70: 2
        1.70 -     1.82: 116
  Bond restraints: 9467
  Sorted by residual:
  bond pdb=" CB  MET B 414 "
       pdb=" CG  MET B 414 "
    ideal  model  delta    sigma   weight residual
    1.520  1.389  0.131 3.00e-02 1.11e+03 1.91e+01
  bond pdb=" CB  TYR A 302 "
       pdb=" CG  TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.512  1.429  0.083 2.20e-02 2.07e+03 1.42e+01
  bond pdb=" CG  TYR A 302 "
       pdb=" CD1 TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.389  1.320  0.069 2.10e-02 2.27e+03 1.07e+01
  bond pdb=" CE1 TYR A 302 "
       pdb=" CZ  TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.378  1.304  0.074 2.40e-02 1.74e+03 9.49e+00
  bond pdb=" CD1 TYR A 302 "
       pdb=" CE1 TYR A 302 "
    ideal  model  delta    sigma   weight residual
    1.382  1.291  0.091 3.00e-02 1.11e+03 9.26e+00
  ... (remaining 9462 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.26: 12470
        4.26 -     8.53: 320
        8.53 -    12.79: 53
       12.79 -    17.05: 15
       17.05 -    21.31: 3
  Bond angle restraints: 12861
  Sorted by residual:
  angle pdb=" C   TYR B 589 "
        pdb=" N   LEU B 593 "
        pdb=" CA  LEU B 593 "
      ideal   model   delta    sigma   weight residual
     121.70  135.34  -13.64 1.80e+00 3.09e-01 5.74e+01
  angle pdb=" C   TYR A 589 "
        pdb=" N   LEU A 593 "
        pdb=" CA  LEU A 593 "
      ideal   model   delta    sigma   weight residual
     121.70  135.33  -13.63 1.80e+00 3.09e-01 5.73e+01
  angle pdb=" CA  TRP A 469 "
        pdb=" CB  TRP A 469 "
        pdb=" CG  TRP A 469 "
      ideal   model   delta    sigma   weight residual
     113.60  127.33  -13.73 1.90e+00 2.77e-01 5.22e+01
  angle pdb=" CA  TYR B 589 "
        pdb=" C   TYR B 589 "
        pdb=" N   LEU B 593 "
      ideal   model   delta    sigma   weight residual
     116.84  128.50  -11.66 1.71e+00 3.42e-01 4.65e+01
  angle pdb=" CA  TYR A 589 "
        pdb=" C   TYR A 589 "
        pdb=" N   LEU A 593 "
      ideal   model   delta    sigma   weight residual
     116.84  128.38  -11.54 1.71e+00 3.42e-01 4.55e+01
  ... (remaining 12856 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.51: 4914
       14.51 -    29.02: 466
       29.02 -    43.53: 120
       43.53 -    58.04: 23
       58.04 -    72.55: 4
  Dihedral angle restraints: 5527
    sinusoidal: 2104
      harmonic: 3423
  Sorted by residual:
  dihedral pdb=" CA  LYS A 324 "
           pdb=" C   LYS A 324 "
           pdb=" N   ASP A 325 "
           pdb=" CA  ASP A 325 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.16  -42.84     0      5.00e+00 4.00e-02 7.34e+01
  dihedral pdb=" CA  LYS B 324 "
           pdb=" C   LYS B 324 "
           pdb=" N   ASP B 325 "
           pdb=" CA  ASP B 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.26  -42.74     0      5.00e+00 4.00e-02 7.31e+01
  dihedral pdb=" CA  ARG B 670 "
           pdb=" C   ARG B 670 "
           pdb=" N   LEU B 671 "
           pdb=" CA  LEU B 671 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -137.73  -42.27     0      5.00e+00 4.00e-02 7.15e+01
  ... (remaining 5524 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.094: 1183
       0.094 -    0.188: 270
       0.188 -    0.282: 47
       0.282 -    0.377: 9
       0.377 -    0.471: 10
  Chirality restraints: 1519
  Sorted by residual:
  chirality pdb=" CG  LEU B 671 "
            pdb=" CB  LEU B 671 "
            pdb=" CD1 LEU B 671 "
            pdb=" CD2 LEU B 671 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.12   -0.47 2.00e-01 2.50e+01 5.54e+00
  chirality pdb=" CA  PHE B 488 "
            pdb=" N   PHE B 488 "
            pdb=" C   PHE B 488 "
            pdb=" CB  PHE B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.25e+00
  chirality pdb=" CG  LEU A 671 "
            pdb=" CB  LEU A 671 "
            pdb=" CD1 LEU A 671 "
            pdb=" CD2 LEU A 671 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.15   -0.44 2.00e-01 2.50e+01 4.83e+00
  ... (remaining 1516 not shown)

  Planarity restraints: 1573
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 517 "    0.068 2.00e-02 2.50e+03   5.24e-02 5.49e+01
        pdb=" CG  TYR B 517 "   -0.127 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 517 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 517 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 517 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 517 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 517 "    0.026 2.00e-02 2.50e+03
        pdb=" OH  TYR B 517 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 517 "    0.068 2.00e-02 2.50e+03   5.22e-02 5.46e+01
        pdb=" CG  TYR A 517 "   -0.126 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 517 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 517 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 517 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 517 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 517 "    0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR A 517 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 469 "   -0.056 2.00e-02 2.50e+03   4.11e-02 4.22e+01
        pdb=" CG  TRP A 469 "    0.110 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 469 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 469 "    0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 469 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 469 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 469 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 469 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 469 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1570 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 535
        2.70 -     3.25: 9654
        3.25 -     3.80: 15800
        3.80 -     4.35: 18494
        4.35 -     4.90: 29057
  Nonbonded interactions: 73540
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 302 "
            pdb=" O   GLU A 291 "
     model   vdw
     2.153 3.040
  nonbonded pdb=" O   ILE B 401 "
            pdb=" OG1 THR B 405 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" O   CYS A 179 "
            pdb=" OG  SER A 183 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   CYS B 179 "
            pdb=" OG  SER B 183 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   CYS A 546 "
            pdb=" OG1 THR A 550 "
     model   vdw
     2.227 3.040
  ... (remaining 73535 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 115 through 671 or resid 819 through 872))
  selection = (chain 'B' and (resid 115 through 671 or resid 819 through 872))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.750
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
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      :  0.010   0.131   9467  Z= 0.438
  Angle     :  1.720  21.313  12861  Z= 0.891
  Chirality :  0.090   0.471   1519
  Planarity :  0.012   0.073   1573
  Dihedral  : 12.748  72.553   3325
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.28 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  8.91 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.73 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 1.59 %

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 are not related in a simple way.
  whole: -4.45 (0.19), residues: 1177
  helix: -2.20 (0.15), residues: 740
  sheet: -3.20 (0.60), residues: 44
  loop : -4.22 (0.23), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 377 
 TYR   0.127   0.007   TYR B 517 
 PHE   0.073   0.006   PHE B 341 
 TRP   0.110   0.008   TRP A 469 
 HIS   0.017   0.003   HIS A 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00957 ( 9467)
  covalent geometry    : angle       1.71980 (12861)
  hydrogen bonds       : bond        0.16569 (  561)
  hydrogen bonds       : angle       7.28631 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 243
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  169 LEU cc_start: 0.9691 (mt) cc_final: 0.9371 (mt)
REVERT: B  246 LEU cc_start: 0.9620 (tp) cc_final: 0.9363 (mt)
REVERT: B  307 PHE cc_start: 0.9541 (t80) cc_final: 0.9098 (t80)
REVERT: B  417 GLU cc_start: 0.9011 (tt0) cc_final: 0.8712 (tm-30)
REVERT: B  464 PHE cc_start: 0.9589 (t80) cc_final: 0.9351 (t80)
REVERT: B  559 MET cc_start: 0.9560 (ptp) cc_final: 0.9271 (ptm)
REVERT: B  565 LEU cc_start: 0.9672 (mt) cc_final: 0.9365 (tt)
REVERT: B  660 LEU cc_start: 0.9761 (tt) cc_final: 0.9553 (mt)
REVERT: B  854 MET cc_start: 0.8638 (tmm) cc_final: 0.8355 (tmm)
REVERT: A  128 MET cc_start: 0.9708 (tpp) cc_final: 0.9054 (tpp)
REVERT: A  143 LEU cc_start: 0.9459 (tp) cc_final: 0.9072 (tp)
REVERT: A  399 PHE cc_start: 0.8710 (m-80) cc_final: 0.8463 (m-80)
REVERT: A  417 GLU cc_start: 0.9197 (tt0) cc_final: 0.8671 (tm-30)
REVERT: A  419 MET cc_start: 0.9507 (mmp) cc_final: 0.9180 (mmt)
REVERT: A  466 MET cc_start: 0.9174 (tpt) cc_final: 0.8960 (tpt)
REVERT: A  473 VAL cc_start: 0.9609 (p) cc_final: 0.9392 (m)
REVERT: A  559 MET cc_start: 0.9558 (ptp) cc_final: 0.9253 (ptm)
REVERT: A  564 ILE cc_start: 0.9757 (mm) cc_final: 0.9505 (mm)
REVERT: A  565 LEU cc_start: 0.9633 (mt) cc_final: 0.9214 (tt)
REVERT: A  854 MET cc_start: 0.8894 (tmm) cc_final: 0.8599 (tmm)
  outliers start: 31
  outliers final: 9
  residues processed: 265
  average time/residue: 0.0788
  time to fit residues: 30.0028
Evaluate side-chains
  164 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 155
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    3.3588

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

Flipped N/Q/H residues before XYZ refinement:
B 369 HIS
B 379 HIS
B 823 GLN
A 379 HIS
A 823 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.058285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.045654 restraints weight = 59392.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.046965 restraints weight = 39301.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.047901 restraints weight = 29027.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.048494 restraints weight = 22974.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049071 restraints weight = 19501.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   9467  Z= 0.255
  Angle     :  0.998  13.603  12861  Z= 0.523
  Chirality :  0.052   0.317   1519
  Planarity :  0.006   0.054   1573
  Dihedral  :  8.355  55.689   1260
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 21.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.94 %
    Favored  : 90.06 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  5.41 %
    Favored  : 94.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.80 %

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 are not related in a simple way.
  whole: -2.55 (0.22), residues: 1177
  helix: -0.57 (0.17), residues: 744
  sheet: -3.26 (0.62), residues: 36
  loop : -3.72 (0.27), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 453 
 TYR   0.026   0.003   TYR A 517 
 PHE   0.059   0.003   PHE B 488 
 TRP   0.038   0.003   TRP A 469 
 HIS   0.009   0.002   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 9467)
  covalent geometry    : angle       0.99777 (12861)
  hydrogen bonds       : bond        0.06241 (  561)
  hydrogen bonds       : angle       5.71163 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 190
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  250 MET cc_start: 0.9126 (tmm) cc_final: 0.8874 (tmm)
REVERT: B  307 PHE cc_start: 0.9441 (t80) cc_final: 0.9207 (t80)
REVERT: B  361 LEU cc_start: 0.9740 (mt) cc_final: 0.9523 (mt)
REVERT: B  410 MET cc_start: 0.9566 (tpt) cc_final: 0.9194 (tpp)
REVERT: B  414 MET cc_start: 0.9326 (tmm) cc_final: 0.9122 (tmm)
REVERT: B  548 GLU cc_start: 0.8720 (pp20) cc_final: 0.8304 (pp20)
REVERT: B  559 MET cc_start: 0.9418 (ptp) cc_final: 0.9156 (ptm)
REVERT: B  564 ILE cc_start: 0.9746 (mm) cc_final: 0.9533 (mm)
REVERT: B  565 LEU cc_start: 0.9629 (mt) cc_final: 0.9297 (tt)
REVERT: B  609 MET cc_start: 0.8946 (mpp) cc_final: 0.8700 (mpp)
REVERT: B  646 MET cc_start: 0.9514 (mmp) cc_final: 0.9227 (mmm)
REVERT: A  235 PHE cc_start: 0.8810 (t80) cc_final: 0.7983 (t80)
REVERT: A  250 MET cc_start: 0.9122 (tmm) cc_final: 0.8773 (tmm)
REVERT: A  399 PHE cc_start: 0.8846 (m-80) cc_final: 0.8277 (m-80)
REVERT: A  404 PHE cc_start: 0.8775 (p90) cc_final: 0.8537 (p90)
REVERT: A  410 MET cc_start: 0.9600 (tpt) cc_final: 0.9151 (tpp)
REVERT: A  466 MET cc_start: 0.8996 (tpt) cc_final: 0.8746 (tpt)
REVERT: A  485 MET cc_start: 0.9443 (mmp) cc_final: 0.8991 (mmm)
REVERT: A  488 PHE cc_start: 0.9201 (m-10) cc_final: 0.8987 (m-10)
REVERT: A  548 GLU cc_start: 0.8642 (pp20) cc_final: 0.8232 (pp20)
REVERT: A  565 LEU cc_start: 0.9613 (mt) cc_final: 0.9265 (tt)
REVERT: A  609 MET cc_start: 0.9081 (mmp) cc_final: 0.8533 (mmp)
REVERT: A  646 MET cc_start: 0.9502 (mmp) cc_final: 0.9190 (mtp)
REVERT: A  854 MET cc_start: 0.8687 (tmm) cc_final: 0.8437 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 194
  average time/residue: 0.0717
  time to fit residues: 20.7858
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 67 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 41 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   chunk 116 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 81 optimal weight:    0.0070
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
** A 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.061316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.048544 restraints weight = 56192.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.049876 restraints weight = 37591.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.050865 restraints weight = 27829.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.051499 restraints weight = 22007.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.052121 restraints weight = 18648.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9467  Z= 0.169
  Angle     :  0.882  10.652  12861  Z= 0.453
  Chirality :  0.048   0.182   1519
  Planarity :  0.005   0.051   1573
  Dihedral  :  7.596  56.803   1260
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  7.01 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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 are not related in a simple way.
  whole: -1.79 (0.23), residues: 1177
  helix:  0.08 (0.18), residues: 757
  sheet: -2.88 (0.76), residues: 34
  loop : -3.65 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 370 
 TYR   0.018   0.002   TYR B 517 
 PHE   0.049   0.002   PHE B 488 
 TRP   0.021   0.002   TRP A 469 
 HIS   0.007   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 9467)
  covalent geometry    : angle       0.88213 (12861)
  hydrogen bonds       : bond        0.05297 (  561)
  hydrogen bonds       : angle       5.21692 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 199
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9322 (mtm) cc_final: 0.8953 (mtp)
REVERT: B  143 LEU cc_start: 0.9252 (tp) cc_final: 0.8982 (pp)
REVERT: B  235 PHE cc_start: 0.8858 (t80) cc_final: 0.7919 (t80)
REVERT: B  250 MET cc_start: 0.9220 (tmm) cc_final: 0.8934 (tmm)
REVERT: B  307 PHE cc_start: 0.9446 (t80) cc_final: 0.9141 (t80)
REVERT: B  410 MET cc_start: 0.9531 (tpt) cc_final: 0.9168 (tpp)
REVERT: B  565 LEU cc_start: 0.9571 (mt) cc_final: 0.9277 (tt)
REVERT: B  567 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9050 (p0)
REVERT: B  646 MET cc_start: 0.9545 (mmp) cc_final: 0.9248 (mmm)
REVERT: B  854 MET cc_start: 0.8537 (tmm) cc_final: 0.8136 (tmm)
REVERT: A  128 MET cc_start: 0.9328 (mtm) cc_final: 0.8970 (mtp)
REVERT: A  164 TRP cc_start: 0.9600 (t-100) cc_final: 0.9174 (t-100)
REVERT: A  235 PHE cc_start: 0.8866 (t80) cc_final: 0.7882 (t80)
REVERT: A  339 MET cc_start: 0.8820 (pmm) cc_final: 0.8418 (pmm)
REVERT: A  399 PHE cc_start: 0.8898 (m-80) cc_final: 0.8274 (m-80)
REVERT: A  410 MET cc_start: 0.9495 (tpt) cc_final: 0.9040 (tpp)
REVERT: A  485 MET cc_start: 0.9507 (mmp) cc_final: 0.9182 (mmm)
REVERT: A  488 PHE cc_start: 0.9317 (m-10) cc_final: 0.9016 (m-10)
REVERT: A  565 LEU cc_start: 0.9543 (mt) cc_final: 0.9177 (tt)
REVERT: A  609 MET cc_start: 0.9212 (mmp) cc_final: 0.8625 (mmp)
REVERT: A  646 MET cc_start: 0.9496 (mmp) cc_final: 0.9177 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 202
  average time/residue: 0.0707
  time to fit residues: 21.3215
Evaluate side-chains
  153 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 150
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 113 optimal weight:    0.0000
   chunk 59 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.061366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.048431 restraints weight = 59457.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.049904 restraints weight = 38667.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.050951 restraints weight = 28060.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.051600 restraints weight = 21853.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.052311 restraints weight = 18397.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9467  Z= 0.158
  Angle     :  0.880  11.766  12861  Z= 0.447
  Chirality :  0.048   0.197   1519
  Planarity :  0.005   0.048   1573
  Dihedral  :  7.218  53.734   1260
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  4.20 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.53 %

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 are not related in a simple way.
  whole: -1.44 (0.24), residues: 1177
  helix:  0.41 (0.18), residues: 763
  sheet: -2.57 (0.73), residues: 44
  loop : -3.77 (0.28), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 370 
 TYR   0.046   0.002   TYR A 589 
 PHE   0.045   0.002   PHE B 488 
 TRP   0.020   0.002   TRP A 469 
 HIS   0.004   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9467)
  covalent geometry    : angle       0.88040 (12861)
  hydrogen bonds       : bond        0.04803 (  561)
  hydrogen bonds       : angle       5.04640 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 198
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9284 (mtm) cc_final: 0.8927 (mtp)
REVERT: B  143 LEU cc_start: 0.9245 (tp) cc_final: 0.8946 (pp)
REVERT: B  174 PHE cc_start: 0.9506 (m-10) cc_final: 0.9223 (m-80)
REVERT: B  235 PHE cc_start: 0.8727 (t80) cc_final: 0.7744 (t80)
REVERT: B  250 MET cc_start: 0.9191 (tmm) cc_final: 0.8936 (tmm)
REVERT: B  307 PHE cc_start: 0.9427 (t80) cc_final: 0.9136 (t80)
REVERT: B  339 MET cc_start: 0.8859 (ptp) cc_final: 0.8619 (ptt)
REVERT: B  374 LEU cc_start: 0.9024 (tp) cc_final: 0.8817 (mt)
REVERT: B  410 MET cc_start: 0.9452 (tpt) cc_final: 0.8989 (tpp)
REVERT: B  609 MET cc_start: 0.9201 (mmp) cc_final: 0.8582 (mmp)
REVERT: B  646 MET cc_start: 0.9574 (mmp) cc_final: 0.9271 (mmm)
REVERT: A  128 MET cc_start: 0.9273 (mtm) cc_final: 0.8893 (mtp)
REVERT: A  164 TRP cc_start: 0.9570 (t-100) cc_final: 0.9313 (t-100)
REVERT: A  178 PHE cc_start: 0.9276 (m-10) cc_final: 0.8927 (m-80)
REVERT: A  235 PHE cc_start: 0.8811 (t80) cc_final: 0.7841 (t80)
REVERT: A  339 MET cc_start: 0.8830 (pmm) cc_final: 0.8497 (pmm)
REVERT: A  399 PHE cc_start: 0.8914 (m-80) cc_final: 0.8275 (m-80)
REVERT: A  400 VAL cc_start: 0.9739 (p) cc_final: 0.9474 (p)
REVERT: A  410 MET cc_start: 0.9355 (tpt) cc_final: 0.8985 (tpp)
REVERT: A  485 MET cc_start: 0.9484 (mmp) cc_final: 0.9253 (mmm)
REVERT: A  488 PHE cc_start: 0.9307 (m-10) cc_final: 0.9019 (m-10)
REVERT: A  565 LEU cc_start: 0.9514 (mt) cc_final: 0.9171 (tt)
REVERT: A  609 MET cc_start: 0.9230 (mmp) cc_final: 0.8735 (mmp)
REVERT: A  646 MET cc_start: 0.9528 (mmp) cc_final: 0.9223 (mtp)
  outliers start: 3
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0731
  time to fit residues: 22.2129
Evaluate side-chains
  150 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 31 optimal weight:    0.0010
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 66 optimal weight:    0.1980
   chunk 27 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 110 optimal weight:    0.0270
   overall best weight:    0.4444

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

Flipped N/Q/H residues before XYZ refinement:
B 379 HIS
A 379 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.062948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.050476 restraints weight = 57603.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.051902 restraints weight = 38291.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.052916 restraints weight = 27996.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.053724 restraints weight = 21929.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.054268 restraints weight = 18032.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.4288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9467  Z= 0.153
  Angle     :  0.855  10.236  12861  Z= 0.429
  Chirality :  0.047   0.169   1519
  Planarity :  0.005   0.050   1573
  Dihedral  :  6.761  43.645   1260
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -1.09 (0.24), residues: 1177
  helix:  0.71 (0.18), residues: 768
  sheet: -2.32 (0.76), residues: 44
  loop : -3.78 (0.28), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 626 
 TYR   0.028   0.002   TYR A 589 
 PHE   0.047   0.002   PHE B 488 
 TRP   0.014   0.001   TRP A 469 
 HIS   0.005   0.001   HIS A 538 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 9467)
  covalent geometry    : angle       0.85508 (12861)
  hydrogen bonds       : bond        0.04571 (  561)
  hydrogen bonds       : angle       4.89358 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9311 (mtm) cc_final: 0.9080 (mtp)
REVERT: B  143 LEU cc_start: 0.9265 (tp) cc_final: 0.8983 (pp)
REVERT: B  174 PHE cc_start: 0.9526 (m-10) cc_final: 0.9250 (m-80)
REVERT: B  235 PHE cc_start: 0.8694 (t80) cc_final: 0.7775 (t80)
REVERT: B  250 MET cc_start: 0.9193 (tmm) cc_final: 0.8962 (tmm)
REVERT: B  307 PHE cc_start: 0.9444 (t80) cc_final: 0.8659 (t80)
REVERT: B  339 MET cc_start: 0.8739 (ptp) cc_final: 0.8389 (ptp)
REVERT: B  396 ILE cc_start: 0.9347 (pt) cc_final: 0.8928 (pt)
REVERT: B  399 PHE cc_start: 0.8864 (m-80) cc_final: 0.8292 (m-80)
REVERT: B  410 MET cc_start: 0.9462 (tpt) cc_final: 0.9071 (tpp)
REVERT: B  470 MET cc_start: 0.8858 (ppp) cc_final: 0.8600 (ppp)
REVERT: B  560 MET cc_start: 0.9251 (mpp) cc_final: 0.9047 (mpp)
REVERT: B  609 MET cc_start: 0.9249 (mmp) cc_final: 0.8622 (mmp)
REVERT: B  646 MET cc_start: 0.9536 (mmp) cc_final: 0.9220 (mmm)
REVERT: A  128 MET cc_start: 0.9305 (mtm) cc_final: 0.8855 (mtp)
REVERT: A  164 TRP cc_start: 0.9554 (t-100) cc_final: 0.9281 (t-100)
REVERT: A  174 PHE cc_start: 0.9486 (m-10) cc_final: 0.9240 (m-80)
REVERT: A  235 PHE cc_start: 0.8699 (t80) cc_final: 0.7702 (t80)
REVERT: A  339 MET cc_start: 0.8877 (pmm) cc_final: 0.8469 (pmm)
REVERT: A  399 PHE cc_start: 0.8857 (m-80) cc_final: 0.8277 (m-80)
REVERT: A  400 VAL cc_start: 0.9764 (p) cc_final: 0.9524 (p)
REVERT: A  410 MET cc_start: 0.9364 (tpt) cc_final: 0.8993 (tpp)
REVERT: A  485 MET cc_start: 0.9510 (mmp) cc_final: 0.9298 (mmm)
REVERT: A  488 PHE cc_start: 0.9355 (m-10) cc_final: 0.9035 (m-10)
REVERT: A  565 LEU cc_start: 0.9479 (mt) cc_final: 0.9151 (tt)
REVERT: A  609 MET cc_start: 0.9183 (mmp) cc_final: 0.8682 (mmp)
REVERT: A  646 MET cc_start: 0.9496 (mmp) cc_final: 0.9185 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0726
  time to fit residues: 22.4708
Evaluate side-chains
  151 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 29 optimal weight:    0.1980
   chunk 76 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 100 optimal weight:   10.0000
   chunk 105 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 115 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 451 HIS
B 827 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.062058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049518 restraints weight = 59635.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.050971 restraints weight = 39312.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.052015 restraints weight = 28742.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.052716 restraints weight = 22436.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.053364 restraints weight = 18750.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9467  Z= 0.154
  Angle     :  0.848  10.102  12861  Z= 0.429
  Chirality :  0.047   0.173   1519
  Planarity :  0.005   0.069   1573
  Dihedral  :  6.572  41.318   1260
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.50 %
    Favored  : 97.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.82 (0.25), residues: 1177
  helix:  0.92 (0.19), residues: 767
  sheet: -2.20 (0.77), residues: 44
  loop : -3.64 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 300 
 TYR   0.021   0.002   TYR A 589 
 PHE   0.046   0.002   PHE B 488 
 TRP   0.019   0.001   TRP B 469 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9467)
  covalent geometry    : angle       0.84756 (12861)
  hydrogen bonds       : bond        0.04503 (  561)
  hydrogen bonds       : angle       4.84897 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9365 (mtm) cc_final: 0.8971 (mtp)
REVERT: B  143 LEU cc_start: 0.9259 (tp) cc_final: 0.8988 (pp)
REVERT: B  174 PHE cc_start: 0.9514 (m-10) cc_final: 0.9266 (m-80)
REVERT: B  235 PHE cc_start: 0.8663 (t80) cc_final: 0.7744 (t80)
REVERT: B  250 MET cc_start: 0.9175 (tmm) cc_final: 0.8950 (tmm)
REVERT: B  399 PHE cc_start: 0.8966 (m-80) cc_final: 0.8413 (m-80)
REVERT: B  410 MET cc_start: 0.9378 (tpt) cc_final: 0.9019 (tpp)
REVERT: B  470 MET cc_start: 0.8842 (ppp) cc_final: 0.8521 (ppp)
REVERT: B  609 MET cc_start: 0.9224 (mmp) cc_final: 0.8577 (mmp)
REVERT: B  646 MET cc_start: 0.9531 (mmp) cc_final: 0.9224 (mmm)
REVERT: A  128 MET cc_start: 0.9305 (mtm) cc_final: 0.8856 (mtp)
REVERT: A  174 PHE cc_start: 0.9422 (m-10) cc_final: 0.9204 (m-80)
REVERT: A  235 PHE cc_start: 0.8655 (t80) cc_final: 0.7668 (t80)
REVERT: A  311 PHE cc_start: 0.8495 (m-80) cc_final: 0.8182 (m-80)
REVERT: A  399 PHE cc_start: 0.8875 (m-80) cc_final: 0.8260 (m-80)
REVERT: A  410 MET cc_start: 0.9266 (tpt) cc_final: 0.8944 (tpp)
REVERT: A  488 PHE cc_start: 0.9336 (m-10) cc_final: 0.9044 (m-10)
REVERT: A  560 MET cc_start: 0.9568 (mtm) cc_final: 0.9257 (mtm)
REVERT: A  609 MET cc_start: 0.9211 (mmp) cc_final: 0.8704 (mmp)
REVERT: A  646 MET cc_start: 0.9498 (mmp) cc_final: 0.9188 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 192
  average time/residue: 0.0688
  time to fit residues: 20.1985
Evaluate side-chains
  139 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 115 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   chunk 34 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:
B 827 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.062201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.049266 restraints weight = 57667.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.050756 restraints weight = 38098.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.051849 restraints weight = 27892.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.052672 restraints weight = 21655.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.053227 restraints weight = 17659.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9467  Z= 0.151
  Angle     :  0.872  12.590  12861  Z= 0.435
  Chirality :  0.047   0.183   1519
  Planarity :  0.005   0.075   1573
  Dihedral  :  6.473  44.230   1260
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.74 (0.25), residues: 1177
  helix:  0.96 (0.19), residues: 765
  sheet: -2.24 (0.87), residues: 34
  loop : -3.51 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 338 
 TYR   0.068   0.002   TYR B 589 
 PHE   0.046   0.002   PHE B 488 
 TRP   0.023   0.002   TRP B 469 
 HIS   0.004   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 9467)
  covalent geometry    : angle       0.87170 (12861)
  hydrogen bonds       : bond        0.04439 (  561)
  hydrogen bonds       : angle       4.81732 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9326 (mtm) cc_final: 0.8939 (mtp)
REVERT: B  143 LEU cc_start: 0.9268 (tp) cc_final: 0.8963 (pp)
REVERT: B  174 PHE cc_start: 0.9508 (m-10) cc_final: 0.9279 (m-80)
REVERT: B  235 PHE cc_start: 0.8658 (t80) cc_final: 0.7732 (t80)
REVERT: B  307 PHE cc_start: 0.9432 (t80) cc_final: 0.8400 (t80)
REVERT: B  399 PHE cc_start: 0.8959 (m-80) cc_final: 0.8420 (m-80)
REVERT: B  410 MET cc_start: 0.9341 (tpt) cc_final: 0.9097 (tpp)
REVERT: B  609 MET cc_start: 0.9233 (mmp) cc_final: 0.8425 (mmp)
REVERT: B  646 MET cc_start: 0.9524 (mmp) cc_final: 0.9215 (mmm)
REVERT: A  128 MET cc_start: 0.9301 (mtm) cc_final: 0.8861 (mtp)
REVERT: A  174 PHE cc_start: 0.9399 (m-10) cc_final: 0.9184 (m-80)
REVERT: A  235 PHE cc_start: 0.8688 (t80) cc_final: 0.7702 (t80)
REVERT: A  339 MET cc_start: 0.8802 (ptp) cc_final: 0.8597 (ptp)
REVERT: A  399 PHE cc_start: 0.8893 (m-80) cc_final: 0.8330 (m-80)
REVERT: A  410 MET cc_start: 0.9263 (tpt) cc_final: 0.8923 (tpp)
REVERT: A  470 MET cc_start: 0.8933 (ppp) cc_final: 0.8723 (ppp)
REVERT: A  488 PHE cc_start: 0.9332 (m-10) cc_final: 0.9094 (m-10)
REVERT: A  609 MET cc_start: 0.9182 (mmp) cc_final: 0.8686 (mmp)
REVERT: A  646 MET cc_start: 0.9492 (mmp) cc_final: 0.9174 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0688
  time to fit residues: 20.0892
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 101 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 32 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
B 838 HIS
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 838 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.061686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.048905 restraints weight = 59290.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.050358 restraints weight = 38940.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.051437 restraints weight = 28297.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.052224 restraints weight = 21965.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.052809 restraints weight = 18001.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9467  Z= 0.163
  Angle     :  0.870  12.009  12861  Z= 0.439
  Chirality :  0.047   0.178   1519
  Planarity :  0.005   0.056   1573
  Dihedral  :  6.347  37.255   1260
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 19.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.77 (0.25), residues: 1177
  helix:  0.92 (0.19), residues: 768
  sheet: -2.23 (0.85), residues: 34
  loop : -3.53 (0.28), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 334 
 TYR   0.052   0.002   TYR B 589 
 PHE   0.048   0.002   PHE B 488 
 TRP   0.030   0.002   TRP B 469 
 HIS   0.007   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 9467)
  covalent geometry    : angle       0.86994 (12861)
  hydrogen bonds       : bond        0.04542 (  561)
  hydrogen bonds       : angle       4.84553 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9299 (mtm) cc_final: 0.8943 (mtp)
REVERT: B  143 LEU cc_start: 0.9190 (tp) cc_final: 0.8914 (pp)
REVERT: B  174 PHE cc_start: 0.9495 (m-10) cc_final: 0.9267 (m-80)
REVERT: B  246 LEU cc_start: 0.9350 (tp) cc_final: 0.9130 (tp)
REVERT: B  311 PHE cc_start: 0.8468 (m-80) cc_final: 0.8153 (m-80)
REVERT: B  399 PHE cc_start: 0.8955 (m-80) cc_final: 0.8398 (m-80)
REVERT: B  410 MET cc_start: 0.9307 (tpt) cc_final: 0.9051 (tpp)
REVERT: B  470 MET cc_start: 0.8831 (ppp) cc_final: 0.8597 (tmm)
REVERT: B  609 MET cc_start: 0.9201 (mmp) cc_final: 0.8557 (mmp)
REVERT: B  646 MET cc_start: 0.9534 (mmp) cc_final: 0.9232 (mmm)
REVERT: A  128 MET cc_start: 0.9306 (mtm) cc_final: 0.8996 (mtp)
REVERT: A  174 PHE cc_start: 0.9404 (m-10) cc_final: 0.9189 (m-80)
REVERT: A  191 ILE cc_start: 0.9738 (pt) cc_final: 0.9383 (mm)
REVERT: A  311 PHE cc_start: 0.8546 (m-80) cc_final: 0.8324 (m-80)
REVERT: A  399 PHE cc_start: 0.8894 (m-80) cc_final: 0.8298 (m-80)
REVERT: A  410 MET cc_start: 0.9252 (tpt) cc_final: 0.8944 (tpp)
REVERT: A  488 PHE cc_start: 0.9363 (m-10) cc_final: 0.9131 (m-10)
REVERT: A  560 MET cc_start: 0.9421 (mtm) cc_final: 0.9159 (mpp)
REVERT: A  609 MET cc_start: 0.9199 (mmp) cc_final: 0.8726 (mmp)
REVERT: A  646 MET cc_start: 0.9518 (mmp) cc_final: 0.9201 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0655
  time to fit residues: 19.1388
Evaluate side-chains
  142 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0970
   chunk 86 optimal weight:    0.4980
   chunk 3 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.062965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.049980 restraints weight = 56925.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.051421 restraints weight = 37704.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.052547 restraints weight = 27357.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.053208 restraints weight = 21323.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.053883 restraints weight = 17885.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.5361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9467  Z= 0.153
  Angle     :  0.884  11.480  12861  Z= 0.437
  Chirality :  0.048   0.203   1519
  Planarity :  0.005   0.055   1573
  Dihedral  :  6.188  36.046   1260
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 17.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.64 (0.25), residues: 1177
  helix:  0.99 (0.19), residues: 772
  sheet: -2.02 (0.88), residues: 34
  loop : -3.45 (0.28), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 338 
 TYR   0.049   0.002   TYR B 589 
 PHE   0.033   0.002   PHE B 484 
 TRP   0.027   0.002   TRP B 469 
 HIS   0.005   0.001   HIS B 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9467)
  covalent geometry    : angle       0.88363 (12861)
  hydrogen bonds       : bond        0.04540 (  561)
  hydrogen bonds       : angle       4.87596 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9256 (mtm) cc_final: 0.8909 (mtp)
REVERT: B  143 LEU cc_start: 0.9242 (tp) cc_final: 0.8940 (pp)
REVERT: B  174 PHE cc_start: 0.9494 (m-10) cc_final: 0.9253 (m-80)
REVERT: B  191 ILE cc_start: 0.9728 (pt) cc_final: 0.9038 (mm)
REVERT: B  246 LEU cc_start: 0.9352 (tp) cc_final: 0.9130 (tp)
REVERT: B  250 MET cc_start: 0.8566 (mmp) cc_final: 0.8360 (mmm)
REVERT: B  311 PHE cc_start: 0.8458 (m-80) cc_final: 0.8153 (m-80)
REVERT: B  399 PHE cc_start: 0.8933 (m-80) cc_final: 0.8380 (m-80)
REVERT: B  410 MET cc_start: 0.9283 (tpt) cc_final: 0.9007 (tpp)
REVERT: B  414 MET cc_start: 0.9216 (tmm) cc_final: 0.8850 (tmm)
REVERT: B  470 MET cc_start: 0.8827 (ppp) cc_final: 0.8576 (tmm)
REVERT: B  609 MET cc_start: 0.9216 (mmp) cc_final: 0.8527 (mmp)
REVERT: B  646 MET cc_start: 0.9528 (mmp) cc_final: 0.9219 (mmm)
REVERT: B  660 LEU cc_start: 0.9572 (tt) cc_final: 0.9330 (mt)
REVERT: A  128 MET cc_start: 0.9301 (mtm) cc_final: 0.8909 (mtp)
REVERT: A  174 PHE cc_start: 0.9396 (m-10) cc_final: 0.9166 (m-80)
REVERT: A  181 LEU cc_start: 0.8286 (mm) cc_final: 0.8057 (pp)
REVERT: A  191 ILE cc_start: 0.9722 (pt) cc_final: 0.9371 (mm)
REVERT: A  311 PHE cc_start: 0.8532 (m-80) cc_final: 0.8256 (m-80)
REVERT: A  319 LEU cc_start: 0.9709 (tp) cc_final: 0.9474 (tp)
REVERT: A  399 PHE cc_start: 0.8814 (m-80) cc_final: 0.8240 (m-80)
REVERT: A  410 MET cc_start: 0.9216 (tpt) cc_final: 0.8876 (tpp)
REVERT: A  488 PHE cc_start: 0.9392 (m-10) cc_final: 0.9153 (m-10)
REVERT: A  609 MET cc_start: 0.9216 (mmp) cc_final: 0.8725 (mmp)
REVERT: A  646 MET cc_start: 0.9521 (mmp) cc_final: 0.9188 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.0704
  time to fit residues: 20.5111
Evaluate side-chains
  141 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 116 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.063355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.050460 restraints weight = 57253.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.051922 restraints weight = 38410.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.053014 restraints weight = 27899.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 16)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.053676 restraints weight = 21699.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.054410 restraints weight = 18001.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.5528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9467  Z= 0.153
  Angle     :  0.892  11.336  12861  Z= 0.439
  Chirality :  0.048   0.189   1519
  Planarity :  0.005   0.051   1573
  Dihedral  :  6.108  33.148   1260
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 18.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.60 (0.25), residues: 1177
  helix:  0.94 (0.19), residues: 774
  sheet: -2.32 (1.02), residues: 24
  loop : -3.21 (0.29), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 334 
 TYR   0.047   0.002   TYR B 589 
 PHE   0.054   0.002   PHE B 488 
 TRP   0.047   0.002   TRP B 433 
 HIS   0.006   0.001   HIS B 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9467)
  covalent geometry    : angle       0.89163 (12861)
  hydrogen bonds       : bond        0.04477 (  561)
  hydrogen bonds       : angle       4.88998 ( 1629)

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

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

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2354 Ramachandran restraints generated.
    1177 Oldfield, 0 Emsley, 1177 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9307 (mtm) cc_final: 0.8944 (mtp)
REVERT: B  143 LEU cc_start: 0.9191 (tp) cc_final: 0.8894 (pp)
REVERT: B  174 PHE cc_start: 0.9459 (m-10) cc_final: 0.9239 (m-80)
REVERT: B  246 LEU cc_start: 0.9368 (tp) cc_final: 0.9150 (tp)
REVERT: B  250 MET cc_start: 0.8596 (mmp) cc_final: 0.8393 (mmm)
REVERT: B  311 PHE cc_start: 0.8461 (m-80) cc_final: 0.8110 (m-80)
REVERT: B  319 LEU cc_start: 0.9702 (tp) cc_final: 0.9439 (tt)
REVERT: B  399 PHE cc_start: 0.8937 (m-80) cc_final: 0.8415 (m-80)
REVERT: B  410 MET cc_start: 0.9292 (tpt) cc_final: 0.9046 (tpp)
REVERT: B  414 MET cc_start: 0.9163 (tmm) cc_final: 0.8788 (tmm)
REVERT: B  432 THR cc_start: 0.9469 (p) cc_final: 0.8959 (p)
REVERT: B  470 MET cc_start: 0.8836 (ppp) cc_final: 0.8615 (tmm)
REVERT: B  609 MET cc_start: 0.9204 (mmp) cc_final: 0.8505 (mmp)
REVERT: B  646 MET cc_start: 0.9494 (mmp) cc_final: 0.9187 (mmm)
REVERT: B  660 LEU cc_start: 0.9556 (tt) cc_final: 0.9312 (mt)
REVERT: A  128 MET cc_start: 0.9317 (mtm) cc_final: 0.8914 (mtp)
REVERT: A  174 PHE cc_start: 0.9346 (m-10) cc_final: 0.9120 (m-80)
REVERT: A  191 ILE cc_start: 0.9714 (pt) cc_final: 0.9044 (mm)
REVERT: A  311 PHE cc_start: 0.8627 (m-80) cc_final: 0.8320 (m-80)
REVERT: A  319 LEU cc_start: 0.9728 (tp) cc_final: 0.9471 (tt)
REVERT: A  399 PHE cc_start: 0.8805 (m-80) cc_final: 0.8245 (m-80)
REVERT: A  410 MET cc_start: 0.9196 (tpt) cc_final: 0.8890 (tpp)
REVERT: A  488 PHE cc_start: 0.9386 (m-10) cc_final: 0.9154 (m-10)
REVERT: A  609 MET cc_start: 0.9211 (mmp) cc_final: 0.8373 (mmp)
REVERT: A  646 MET cc_start: 0.9490 (mmp) cc_final: 0.9164 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0697
  time to fit residues: 20.7390
Evaluate side-chains
  146 residues out of total 999 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.4980
   chunk 52 optimal weight:    0.0870
   chunk 25 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 104 optimal weight:    8.9990
   chunk 42 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 2 optimal weight:    5.9990
   chunk 11 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
B 827 GLN
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.063832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.050908 restraints weight = 56516.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.052391 restraints weight = 37639.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.053528 restraints weight = 27331.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.054326 restraints weight = 21349.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.054966 restraints weight = 17483.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9467  Z= 0.155
  Angle     :  0.887  11.137  12861  Z= 0.440
  Chirality :  0.048   0.212   1519
  Planarity :  0.005   0.050   1573
  Dihedral  :  5.981  31.000   1260
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.50 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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 are not related in a simple way.
  whole: -0.53 (0.25), residues: 1177
  helix:  1.00 (0.19), residues: 767
  sheet: -2.17 (1.05), residues: 24
  loop : -3.12 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 334 
 TYR   0.044   0.002   TYR B 589 
 PHE   0.022   0.002   PHE A 306 
 TRP   0.041   0.002   TRP B 433 
 HIS   0.006   0.001   HIS B 555 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9467)
  covalent geometry    : angle       0.88735 (12861)
  hydrogen bonds       : bond        0.04431 (  561)
  hydrogen bonds       : angle       4.92875 ( 1629)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1564.87 seconds
wall clock time: 27 minutes 41.51 seconds (1661.51 seconds total)