Starting phenix.real_space_refine
on Tue Mar  3 16:55:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qv6_4645/03_2026/6qv6_4645.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    4814      2.51       5
     N    1138      2.21       5
     O    1198      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 7208
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 3604
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3604
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 25, 'TRANS': 443}
          Chain breaks: 1
  Restraints were copied for chains:
    A
  Time building chain proxies: 2.57, per 1000 atoms: 0.36
  Number of scatterers: 7208
  At special positions: 0
  Unit cell: (105.93, 82.39, 75.97, 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      58     16.00
     O    1198      8.00
     N    1138      7.00
     C    4814      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: 0.53
  Conformation dependent library (CDL) restraints added in 274.6 milliseconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 2 sheets defined
      74.8% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 116 through 153
      removed outlier: 4.096A  pdb=" N   PHE B 120 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU B 130 " --> pdb=" O   LEU B 126 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 198
      removed outlier: 4.209A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 207
      removed outlier: 3.852A  pdb=" N   LEU B 207 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 204 through 207'
    Processing helix  chain 'B' and resid 208 through 224
      removed outlier: 3.962A  pdb=" N   PHE B 212 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.644A  pdb=" N   PHE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    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: 3.879A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL B 321 " --> pdb=" O   ARG B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 377
      removed outlier: 3.899A  pdb=" N   PHE B 351 " --> pdb=" O   GLU B 347 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
      removed outlier: 3.585A  pdb=" N   HIS B 389 " --> pdb=" O   PHE B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 404
      removed outlier: 3.645A  pdb=" N   GLY B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   VAL B 397 " --> pdb=" O   TYR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 427
    Processing helix  chain 'B' and resid 434 through 438
      removed outlier: 3.806A  pdb=" N   GLY B 438 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.682A  pdb=" N   ALA B 447 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.597A  pdb=" N   ILE B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   MET B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 537
      removed outlier: 4.761A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 541 through 551
      removed outlier: 3.903A  pdb=" N   ILE B 545 " --> pdb=" O   SER B 541 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
      removed outlier: 3.731A  pdb=" N   GLN B 574 " --> pdb=" O   ALA B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 586
    Processing helix  chain 'A' and resid 116 through 153
      removed outlier: 4.097A  pdb=" N   PHE A 120 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LEU A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 198
      removed outlier: 4.209A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 207
      removed outlier: 3.852A  pdb=" N   LEU A 207 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 204 through 207'
    Processing helix  chain 'A' and resid 208 through 224
      removed outlier: 3.963A  pdb=" N   PHE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.644A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    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: 3.879A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 377
      removed outlier: 3.900A  pdb=" N   PHE A 351 " --> pdb=" O   GLU A 347 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 3.585A  pdb=" N   HIS A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 404
      removed outlier: 3.645A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL A 397 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 434 through 438
      removed outlier: 3.807A  pdb=" N   GLY A 438 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.681A  pdb=" N   ALA A 447 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.598A  pdb=" N   ILE A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   MET A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 537
      removed outlier: 4.761A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 551
      removed outlier: 3.904A  pdb=" N   ILE A 545 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
      removed outlier: 3.732A  pdb=" N   GLN A 574 " --> pdb=" O   ALA A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 586
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'A' and resid 510 through 512

    486 hydrogen bonds defined for protein.
    1422 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: 1.06

  Time building geometry restraints manager: 0.74 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: 2036
        1.34 -     1.46: 1662
        1.46 -     1.58: 3614
        1.58 -     1.69: 0
        1.69 -     1.81: 98
  Bond restraints: 7410
  Sorted by residual:
  bond pdb=" CB  PRO B 408 "
       pdb=" CG  PRO B 408 "
    ideal  model  delta    sigma   weight residual
    1.492  1.400  0.092 5.00e-02 4.00e+02 3.37e+00
  bond pdb=" CB  PRO A 408 "
       pdb=" CG  PRO A 408 "
    ideal  model  delta    sigma   weight residual
    1.492  1.401  0.091 5.00e-02 4.00e+02 3.31e+00
  bond pdb=" CB  GLU B 347 "
       pdb=" CG  GLU B 347 "
    ideal  model  delta    sigma   weight residual
    1.520  1.575 -0.055 3.00e-02 1.11e+03 3.30e+00
  bond pdb=" CB  GLU A 347 "
       pdb=" CG  GLU A 347 "
    ideal  model  delta    sigma   weight residual
    1.520  1.574 -0.054 3.00e-02 1.11e+03 3.26e+00
  bond pdb=" CG1 ILE A 564 "
       pdb=" CD1 ILE A 564 "
    ideal  model  delta    sigma   weight residual
    1.513  1.443  0.070 3.90e-02 6.57e+02 3.24e+00
  ... (remaining 7405 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.00: 9692
        3.00 -     6.00: 330
        6.00 -     9.00: 36
        9.00 -    12.00: 20
       12.00 -    15.00: 6
  Bond angle restraints: 10084
  Sorted by residual:
  angle pdb=" CA  GLU B 347 "
        pdb=" CB  GLU B 347 "
        pdb=" CG  GLU B 347 "
      ideal   model   delta    sigma   weight residual
     114.10  129.10  -15.00 2.00e+00 2.50e-01 5.62e+01
  angle pdb=" CA  GLU A 347 "
        pdb=" CB  GLU A 347 "
        pdb=" CG  GLU A 347 "
      ideal   model   delta    sigma   weight residual
     114.10  129.07  -14.97 2.00e+00 2.50e-01 5.60e+01
  angle pdb=" CB  GLU A 347 "
        pdb=" CG  GLU A 347 "
        pdb=" CD  GLU A 347 "
      ideal   model   delta    sigma   weight residual
     112.60  122.08   -9.48 1.70e+00 3.46e-01 3.11e+01
  angle pdb=" CB  GLU B 347 "
        pdb=" CG  GLU B 347 "
        pdb=" CD  GLU B 347 "
      ideal   model   delta    sigma   weight residual
     112.60  122.03   -9.43 1.70e+00 3.46e-01 3.08e+01
  angle pdb=" N   VAL A 252 "
        pdb=" CA  VAL A 252 "
        pdb=" C   VAL A 252 "
      ideal   model   delta    sigma   weight residual
     113.20  107.91    5.29 9.60e-01 1.09e+00 3.03e+01
  ... (remaining 10079 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.85: 3848
       13.85 -    27.70: 328
       27.70 -    41.56: 86
       41.56 -    55.41: 16
       55.41 -    69.26: 4
  Dihedral angle restraints: 4282
    sinusoidal: 1600
      harmonic: 2682
  Sorted by residual:
  dihedral pdb=" CA  ALA A 326 "
           pdb=" C   ALA A 326 "
           pdb=" N   VAL A 327 "
           pdb=" CA  VAL A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.24  -45.76     0      5.00e+00 4.00e-02 8.37e+01
  dihedral pdb=" CA  ALA B 326 "
           pdb=" C   ALA B 326 "
           pdb=" N   VAL B 327 "
           pdb=" CA  VAL B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.27  -45.73     0      5.00e+00 4.00e-02 8.36e+01
  dihedral pdb=" CA  ILE A 290 "
           pdb=" C   ILE A 290 "
           pdb=" N   GLU A 291 "
           pdb=" CA  GLU A 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.85  -28.15     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 4279 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 718
       0.053 -    0.107: 318
       0.107 -    0.160: 101
       0.160 -    0.214: 37
       0.214 -    0.267: 4
  Chirality restraints: 1178
  Sorted by residual:
  chirality pdb=" CB  ILE A 329 "
            pdb=" CA  ILE A 329 "
            pdb=" CG1 ILE A 329 "
            pdb=" CG2 ILE A 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" CB  ILE B 329 "
            pdb=" CA  ILE B 329 "
            pdb=" CG1 ILE B 329 "
            pdb=" CG2 ILE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  LEU B 557 "
            pdb=" N   LEU B 557 "
            pdb=" C   LEU B 557 "
            pdb=" CB  LEU B 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1175 not shown)

  Planarity restraints: 1234
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 365 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   PHE B 365 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   PHE B 365 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL B 366 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 365 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.21e+00
        pdb=" C   PHE A 365 "    0.052 2.00e-02 2.50e+03
        pdb=" O   PHE A 365 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   VAL A 366 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 370 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.40e+00
        pdb=" C   ARG A 370 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   ARG A 370 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLN A 371 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1231 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2041
        2.81 -     3.33: 7042
        3.33 -     3.85: 12078
        3.85 -     4.38: 12824
        4.38 -     4.90: 22442
  Nonbonded interactions: 56427
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OE2 GLU B 193 "
            pdb=" OH  TYR B 206 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OE2 GLU A 193 "
            pdb=" OH  TYR A 206 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OE2 GLU B 291 "
            pdb=" OG  SER B 541 "
     model   vdw
     2.296 3.040
  ... (remaining 56422 not shown)

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

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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.660
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
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   0.092   7410  Z= 0.399
  Angle     :  1.309  14.996  10084  Z= 0.693
  Chirality :  0.070   0.267   1178
  Planarity :  0.011   0.059   1234
  Dihedral  : 11.643  69.261   2562
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  7.96 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  6.77 %
    Favored  : 92.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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: -4.57 (0.21), residues: 930
  helix: -2.34 (0.16), residues: 672
  sheet:  None (None), residues: 0
  loop : -4.55 (0.28), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 390 
 TYR   0.035   0.003   TYR B 146 
 PHE   0.026   0.004   PHE B 547 
 TRP   0.019   0.003   TRP B 133 
 HIS   0.009   0.002   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00969 ( 7410)
  covalent geometry    : angle       1.30897 (10084)
  hydrogen bonds       : bond        0.17130 (  486)
  hydrogen bonds       : angle       7.14507 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 156
  time to evaluate  : 0.266 
Fit side-chains
REVERT: B  194 MET cc_start: 0.8534 (ppp) cc_final: 0.8308 (ppp)
REVERT: B  209 MET cc_start: 0.8955 (tmt) cc_final: 0.8635 (tmm)
REVERT: B  291 GLU cc_start: 0.8040 (pm20) cc_final: 0.7626 (pm20)
REVERT: B  417 GLU cc_start: 0.8383 (tt0) cc_final: 0.8007 (tm-30)
REVERT: B  571 GLN cc_start: 0.8664 (tt0) cc_final: 0.8001 (tp40)
REVERT: B  589 TYR cc_start: 0.8083 (t80) cc_final: 0.7697 (t80)
REVERT: A  206 TYR cc_start: 0.6453 (t80) cc_final: 0.6239 (t80)
REVERT: A  209 MET cc_start: 0.8905 (tmt) cc_final: 0.8545 (tmm)
REVERT: A  589 TYR cc_start: 0.8060 (t80) cc_final: 0.7589 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 162
  average time/residue: 0.0754
  time to fit residues: 16.7409
Evaluate side-chains
  108 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  347 GLU
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  347 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0670
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.093693 restraints weight = 14632.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.097504 restraints weight = 6593.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.099916 restraints weight = 3832.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.101331 restraints weight = 2657.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.102679 restraints weight = 2084.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7410  Z= 0.148
  Angle     :  0.776  10.388  10084  Z= 0.390
  Chirality :  0.044   0.166   1178
  Planarity :  0.006   0.053   1234
  Dihedral  :  6.385  39.105    996
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.15 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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: -1.78 (0.27), residues: 930
  helix: -0.12 (0.20), residues: 652
  sheet:  None (None), residues: 0
  loop : -3.74 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 199 
 TYR   0.015   0.001   TYR B 206 
 PHE   0.034   0.002   PHE A 547 
 TRP   0.015   0.001   TRP B 469 
 HIS   0.004   0.001   HIS A 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7410)
  covalent geometry    : angle       0.77629 (10084)
  hydrogen bonds       : bond        0.05358 (  486)
  hydrogen bonds       : angle       4.46418 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 161
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: B  194 MET cc_start: 0.8434 (ppp) cc_final: 0.8228 (ppp)
REVERT: B  209 MET cc_start: 0.8907 (tmt) cc_final: 0.8426 (tmm)
REVERT: B  291 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7592 (pm20)
REVERT: B  340 ASP cc_start: 0.7556 (m-30) cc_final: 0.7299 (m-30)
REVERT: B  344 ASP cc_start: 0.8600 (p0) cc_final: 0.8375 (p0)
REVERT: B  571 GLN cc_start: 0.8547 (tt0) cc_final: 0.7877 (tp40)
REVERT: A  209 MET cc_start: 0.8909 (tmt) cc_final: 0.8441 (tmm)
REVERT: A  291 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7788 (pm20)
REVERT: A  332 LEU cc_start: 0.8094 (tp) cc_final: 0.7880 (tp)
REVERT: A  340 ASP cc_start: 0.8025 (m-30) cc_final: 0.7816 (m-30)
REVERT: A  344 ASP cc_start: 0.8788 (p0) cc_final: 0.8557 (p0)
REVERT: A  466 MET cc_start: 0.7701 (mmt) cc_final: 0.7371 (mmt)
REVERT: A  571 GLN cc_start: 0.8385 (tt0) cc_final: 0.7785 (tp40)
  outliers start: 28
  outliers final: 10
  residues processed: 179
  average time/residue: 0.0526
  time to fit residues: 14.2648
Evaluate side-chains
  130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  389 HIS
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 73 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 301 ASN
** B 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 = 0.3512 r_free = 0.3512 target = 0.109891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.092586 restraints weight = 14353.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096290 restraints weight = 6474.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.098588 restraints weight = 3788.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.100389 restraints weight = 2649.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101599 restraints weight = 2010.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7410  Z= 0.147
  Angle     :  0.773  12.199  10084  Z= 0.379
  Chirality :  0.044   0.190   1178
  Planarity :  0.005   0.046   1234
  Dihedral  :  5.367  34.789    986
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 18.49 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.23 %

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 (0.28), residues: 930
  helix:  0.78 (0.21), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.89 (0.32), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 199 
 TYR   0.016   0.001   TYR A 524 
 PHE   0.032   0.002   PHE A 547 
 TRP   0.011   0.001   TRP B 164 
 HIS   0.010   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7410)
  covalent geometry    : angle       0.77297 (10084)
  hydrogen bonds       : bond        0.04756 (  486)
  hydrogen bonds       : angle       4.06775 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8780 (tp)
REVERT: B  178 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.7965 (t80)
REVERT: B  209 MET cc_start: 0.8874 (tmt) cc_final: 0.8341 (tmm)
REVERT: B  291 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7621 (pm20)
REVERT: B  391 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8782 (pp)
REVERT: B  469 TRP cc_start: 0.8120 (p-90) cc_final: 0.7784 (p-90)
REVERT: B  571 GLN cc_start: 0.8499 (tt0) cc_final: 0.7864 (tp40)
REVERT: A  127 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8828 (tp)
REVERT: A  178 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: A  209 MET cc_start: 0.8879 (tmt) cc_final: 0.8366 (tmm)
REVERT: A  303 TRP cc_start: 0.8295 (m-10) cc_final: 0.8085 (m-10)
REVERT: A  391 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8524 (pp)
REVERT: A  466 MET cc_start: 0.7758 (mmt) cc_final: 0.7438 (mmt)
REVERT: A  571 GLN cc_start: 0.8475 (tt0) cc_final: 0.7789 (tp40)
  outliers start: 40
  outliers final: 25
  residues processed: 154
  average time/residue: 0.0519
  time to fit residues: 12.2449
Evaluate side-chains
  145 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  389 HIS
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 7 optimal weight:    0.4980
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 84 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 451 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.110459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.092828 restraints weight = 14598.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096595 restraints weight = 6630.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.098980 restraints weight = 3883.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.100722 restraints weight = 2704.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.101952 restraints weight = 2073.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7410  Z= 0.137
  Angle     :  0.732  11.496  10084  Z= 0.356
  Chirality :  0.043   0.173   1178
  Planarity :  0.005   0.046   1234
  Dihedral  :  5.021  30.354    986
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  7.03 %
    Allowed  : 17.06 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -0.27 (0.29), residues: 930
  helix:  1.15 (0.21), residues: 664
  sheet:  None (None), residues: 0
  loop : -3.80 (0.32), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 199 
 TYR   0.012   0.001   TYR B 206 
 PHE   0.029   0.001   PHE A 547 
 TRP   0.014   0.001   TRP A 148 
 HIS   0.009   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7410)
  covalent geometry    : angle       0.73201 (10084)
  hydrogen bonds       : bond        0.04335 (  486)
  hydrogen bonds       : angle       3.87947 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 125
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8767 (tp)
REVERT: B  178 PHE cc_start: 0.8316 (OUTLIER) cc_final: 0.7964 (t80)
REVERT: B  209 MET cc_start: 0.8860 (tmt) cc_final: 0.8342 (tmm)
REVERT: B  368 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9157 (mm)
REVERT: B  389 HIS cc_start: 0.8117 (OUTLIER) cc_final: 0.7770 (m-70)
REVERT: B  391 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8692 (pp)
REVERT: B  466 MET cc_start: 0.7615 (mmt) cc_final: 0.7190 (mmp)
REVERT: B  571 GLN cc_start: 0.8470 (tt0) cc_final: 0.7788 (tp40)
REVERT: A  127 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8801 (tp)
REVERT: A  178 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7954 (t80)
REVERT: A  209 MET cc_start: 0.8856 (tmt) cc_final: 0.8334 (tmm)
REVERT: A  302 TYR cc_start: 0.9151 (t80) cc_final: 0.8412 (t80)
REVERT: A  368 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9077 (mm)
REVERT: A  391 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8434 (pp)
REVERT: A  466 MET cc_start: 0.7832 (mmt) cc_final: 0.7493 (mmt)
REVERT: A  571 GLN cc_start: 0.8432 (tt0) cc_final: 0.7813 (tp40)
  outliers start: 54
  outliers final: 28
  residues processed: 163
  average time/residue: 0.0546
  time to fit residues: 13.6608
Evaluate side-chains
  149 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 112
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  368 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  389 HIS
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 3 optimal weight:    0.3980
   chunk 17 optimal weight:    0.0370
   chunk 86 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094794 restraints weight = 14300.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.098552 restraints weight = 6493.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.100918 restraints weight = 3822.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.102796 restraints weight = 2669.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.103969 restraints weight = 2037.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7410  Z= 0.128
  Angle     :  0.709  12.803  10084  Z= 0.345
  Chirality :  0.042   0.176   1178
  Planarity :  0.005   0.049   1234
  Dihedral  :  4.804  26.093    986
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 20.05 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.29), residues: 930
  helix:  1.27 (0.21), residues: 670
  sheet:  None (None), residues: 0
  loop : -3.61 (0.33), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 199 
 TYR   0.013   0.001   TYR B 524 
 PHE   0.028   0.001   PHE A 547 
 TRP   0.012   0.001   TRP A 469 
 HIS   0.008   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7410)
  covalent geometry    : angle       0.70934 (10084)
  hydrogen bonds       : bond        0.04029 (  486)
  hydrogen bonds       : angle       3.77131 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  178 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7995 (t80)
REVERT: B  209 MET cc_start: 0.8848 (tmt) cc_final: 0.8320 (tmm)
REVERT: B  287 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8720 (mp)
REVERT: B  302 TYR cc_start: 0.9059 (t80) cc_final: 0.8347 (t80)
REVERT: B  303 TRP cc_start: 0.8463 (m-10) cc_final: 0.8061 (m100)
REVERT: B  466 MET cc_start: 0.7607 (mmt) cc_final: 0.7219 (mmp)
REVERT: B  571 GLN cc_start: 0.8471 (tt0) cc_final: 0.7837 (tp40)
REVERT: A  127 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8781 (tp)
REVERT: A  178 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7837 (t80)
REVERT: A  209 MET cc_start: 0.8884 (tmt) cc_final: 0.8399 (tmm)
REVERT: A  302 TYR cc_start: 0.9157 (t80) cc_final: 0.8359 (t80)
REVERT: A  368 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9114 (mm)
REVERT: A  571 GLN cc_start: 0.8442 (tt0) cc_final: 0.7831 (tp40)
  outliers start: 39
  outliers final: 22
  residues processed: 152
  average time/residue: 0.0554
  time to fit residues: 13.2435
Evaluate side-chains
  142 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  557 LEU
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  127 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 40 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    0.1980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.108919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.091091 restraints weight = 14401.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.094641 restraints weight = 6662.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.097114 restraints weight = 4003.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.098770 restraints weight = 2803.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.100081 restraints weight = 2173.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7410  Z= 0.155
  Angle     :  0.748  12.130  10084  Z= 0.363
  Chirality :  0.043   0.180   1178
  Planarity :  0.005   0.048   1234
  Dihedral  :  4.759  23.629    986
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  6.51 %
    Allowed  : 20.31 %
    Favored  : 73.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.29), residues: 930
  helix:  1.42 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.45 (0.33), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 199 
 TYR   0.011   0.001   TYR B 137 
 PHE   0.028   0.002   PHE B 174 
 TRP   0.012   0.001   TRP B 148 
 HIS   0.007   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 7410)
  covalent geometry    : angle       0.74805 (10084)
  hydrogen bonds       : bond        0.04373 (  486)
  hydrogen bonds       : angle       3.74728 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8806 (tp)
REVERT: B  178 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: B  209 MET cc_start: 0.8888 (tmt) cc_final: 0.8375 (tmm)
REVERT: B  291 GLU cc_start: 0.7901 (pm20) cc_final: 0.7618 (pm20)
REVERT: B  391 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8730 (pp)
REVERT: B  466 MET cc_start: 0.7662 (mmt) cc_final: 0.7391 (mmp)
REVERT: B  571 GLN cc_start: 0.8434 (tt0) cc_final: 0.7833 (tp40)
REVERT: A  178 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8014 (t80)
REVERT: A  209 MET cc_start: 0.8919 (tmt) cc_final: 0.8460 (tmm)
REVERT: A  302 TYR cc_start: 0.9150 (t80) cc_final: 0.8327 (t80)
REVERT: A  328 THR cc_start: 0.7123 (m) cc_final: 0.6772 (t)
REVERT: A  368 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9126 (mm)
REVERT: A  391 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (pp)
REVERT: A  466 MET cc_start: 0.7746 (mmt) cc_final: 0.7367 (mmp)
REVERT: A  571 GLN cc_start: 0.8484 (tt0) cc_final: 0.7858 (tp40)
  outliers start: 50
  outliers final: 32
  residues processed: 151
  average time/residue: 0.0530
  time to fit residues: 12.1356
Evaluate side-chains
  148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 110
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.105908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.088027 restraints weight = 14764.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.091577 restraints weight = 6849.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.093886 restraints weight = 4102.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.095606 restraints weight = 2904.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096142 restraints weight = 2250.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   7410  Z= 0.192
  Angle     :  0.777  11.970  10084  Z= 0.380
  Chirality :  0.045   0.188   1178
  Planarity :  0.005   0.047   1234
  Dihedral  :  4.862  24.609    986
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 20.83 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.29), residues: 930
  helix:  1.42 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.44 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 338 
 TYR   0.013   0.001   TYR B 146 
 PHE   0.029   0.002   PHE B 174 
 TRP   0.013   0.001   TRP B 148 
 HIS   0.008   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 7410)
  covalent geometry    : angle       0.77744 (10084)
  hydrogen bonds       : bond        0.04753 (  486)
  hydrogen bonds       : angle       3.80227 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 111
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  127 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8903 (tp)
REVERT: B  178 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7984 (t80)
REVERT: B  209 MET cc_start: 0.8935 (tmt) cc_final: 0.8427 (tmm)
REVERT: B  291 GLU cc_start: 0.7870 (pm20) cc_final: 0.7615 (pm20)
REVERT: B  391 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8705 (pp)
REVERT: B  466 MET cc_start: 0.7746 (mmt) cc_final: 0.7349 (mmp)
REVERT: B  571 GLN cc_start: 0.8527 (tt0) cc_final: 0.7898 (tp40)
REVERT: A  178 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7964 (t80)
REVERT: A  209 MET cc_start: 0.8968 (tmt) cc_final: 0.8527 (tmm)
REVERT: A  302 TYR cc_start: 0.9171 (t80) cc_final: 0.8261 (t80)
REVERT: A  368 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9239 (mm)
REVERT: A  391 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8494 (pp)
REVERT: A  571 GLN cc_start: 0.8530 (tt0) cc_final: 0.7924 (tp40)
  outliers start: 55
  outliers final: 37
  residues processed: 148
  average time/residue: 0.0559
  time to fit residues: 12.7534
Evaluate side-chains
  151 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 108
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  127 LEU
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  519 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain B residue  567 ASN
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  424 ILE
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 89 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0770
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 50 optimal weight:    0.2980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.109974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.092201 restraints weight = 14750.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.095855 restraints weight = 6791.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.098289 restraints weight = 4041.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.099942 restraints weight = 2837.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.101270 restraints weight = 2199.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7410  Z= 0.131
  Angle     :  0.714  12.465  10084  Z= 0.346
  Chirality :  0.042   0.185   1178
  Planarity :  0.005   0.050   1234
  Dihedral  :  4.703  22.503    986
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.92 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.29), residues: 930
  helix:  1.53 (0.21), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.23 (0.34), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 334 
 TYR   0.012   0.001   TYR B 524 
 PHE   0.028   0.001   PHE A 547 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.007   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7410)
  covalent geometry    : angle       0.71351 (10084)
  hydrogen bonds       : bond        0.04036 (  486)
  hydrogen bonds       : angle       3.66836 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8814 (tpp) cc_final: 0.8601 (tpt)
REVERT: B  178 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.8042 (t80)
REVERT: B  209 MET cc_start: 0.8899 (tmt) cc_final: 0.8408 (tmm)
REVERT: B  302 TYR cc_start: 0.9086 (t80) cc_final: 0.8344 (t80)
REVERT: B  303 TRP cc_start: 0.8460 (m-10) cc_final: 0.8019 (m100)
REVERT: B  328 THR cc_start: 0.6573 (m) cc_final: 0.6267 (t)
REVERT: B  391 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8671 (pp)
REVERT: B  436 HIS cc_start: 0.7997 (m-70) cc_final: 0.7684 (m-70)
REVERT: B  466 MET cc_start: 0.7605 (mmt) cc_final: 0.7174 (mmp)
REVERT: B  571 GLN cc_start: 0.8473 (tt0) cc_final: 0.7846 (tp40)
REVERT: A  178 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (t80)
REVERT: A  209 MET cc_start: 0.8918 (tmt) cc_final: 0.8429 (tmm)
REVERT: A  302 TYR cc_start: 0.9170 (t80) cc_final: 0.8310 (t80)
REVERT: A  328 THR cc_start: 0.7086 (m) cc_final: 0.6774 (t)
REVERT: A  368 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9124 (mm)
REVERT: A  391 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8527 (pp)
REVERT: A  571 GLN cc_start: 0.8402 (tt0) cc_final: 0.7790 (tp40)
  outliers start: 34
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0566
  time to fit residues: 12.6497
Evaluate side-chains
  150 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  403 SER
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Chi-restraints excluded: chain A residue  567 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 81 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0670
   chunk 58 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 379 HIS
** A 237 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 = 0.3527 r_free = 0.3527 target = 0.110624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.092823 restraints weight = 14369.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.096460 restraints weight = 6646.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.098897 restraints weight = 3968.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.100346 restraints weight = 2789.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.101725 restraints weight = 2206.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.4118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7410  Z= 0.133
  Angle     :  0.714  12.573  10084  Z= 0.346
  Chirality :  0.042   0.184   1178
  Planarity :  0.005   0.051   1234
  Dihedral  :  4.716  21.922    986
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 22.14 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.29), residues: 930
  helix:  1.63 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.18 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 334 
 TYR   0.011   0.001   TYR B 206 
 PHE   0.029   0.001   PHE B 174 
 TRP   0.013   0.001   TRP A 469 
 HIS   0.008   0.001   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 7410)
  covalent geometry    : angle       0.71375 (10084)
  hydrogen bonds       : bond        0.04014 (  486)
  hydrogen bonds       : angle       3.62524 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 125
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8856 (tpp) cc_final: 0.8629 (tpt)
REVERT: B  178 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.8042 (t80)
REVERT: B  209 MET cc_start: 0.8898 (tmt) cc_final: 0.8417 (tmm)
REVERT: B  291 GLU cc_start: 0.8115 (pm20) cc_final: 0.7842 (pm20)
REVERT: B  302 TYR cc_start: 0.9073 (t80) cc_final: 0.8345 (t80)
REVERT: B  303 TRP cc_start: 0.8442 (m-10) cc_final: 0.8007 (m100)
REVERT: B  328 THR cc_start: 0.6717 (m) cc_final: 0.6358 (t)
REVERT: B  339 MET cc_start: 0.7890 (ptp) cc_final: 0.7530 (ptp)
REVERT: B  391 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8661 (pp)
REVERT: B  422 GLU cc_start: 0.8441 (pm20) cc_final: 0.8234 (pm20)
REVERT: B  436 HIS cc_start: 0.7949 (m-70) cc_final: 0.7598 (m-70)
REVERT: B  571 GLN cc_start: 0.8400 (tt0) cc_final: 0.7805 (tp40)
REVERT: A  128 MET cc_start: 0.8768 (tpp) cc_final: 0.8531 (tpt)
REVERT: A  178 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7991 (t80)
REVERT: A  209 MET cc_start: 0.8920 (tmt) cc_final: 0.8484 (tmm)
REVERT: A  302 TYR cc_start: 0.9160 (t80) cc_final: 0.8326 (t80)
REVERT: A  328 THR cc_start: 0.7040 (m) cc_final: 0.6690 (t)
REVERT: A  368 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9126 (mm)
REVERT: A  391 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8526 (pp)
REVERT: A  404 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8682 (m-80)
REVERT: A  571 GLN cc_start: 0.8367 (tt0) cc_final: 0.7789 (tp40)
  outliers start: 39
  outliers final: 29
  residues processed: 149
  average time/residue: 0.0506
  time to fit residues: 11.6517
Evaluate side-chains
  154 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  162 LEU
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  178 PHE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  564 ILE
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  404 PHE
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  454 VAL
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  564 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 17 optimal weight:    0.0980
   chunk 83 optimal weight:    0.3980
   chunk 77 optimal weight:    0.1980
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0070
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.2998

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.112989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.095046 restraints weight = 14398.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.098791 restraints weight = 6634.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.101271 restraints weight = 3938.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.103067 restraints weight = 2753.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.104181 restraints weight = 2114.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.4327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7410  Z= 0.128
  Angle     :  0.719  13.100  10084  Z= 0.346
  Chirality :  0.042   0.183   1178
  Planarity :  0.005   0.054   1234
  Dihedral  :  4.596  21.830    986
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.31 %
    Favored  : 72.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.29), residues: 930
  helix:  1.81 (0.21), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.77 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 334 
 TYR   0.017   0.001   TYR B 524 
 PHE   0.029   0.001   PHE B 174 
 TRP   0.016   0.001   TRP A 469 
 HIS   0.007   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7410)
  covalent geometry    : angle       0.71859 (10084)
  hydrogen bonds       : bond        0.03704 (  486)
  hydrogen bonds       : angle       3.58220 ( 1422)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8769 (tpp) cc_final: 0.8549 (tpt)
REVERT: B  209 MET cc_start: 0.8899 (tmt) cc_final: 0.8417 (tmm)
REVERT: B  291 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (pm20)
REVERT: B  302 TYR cc_start: 0.9074 (t80) cc_final: 0.8422 (t80)
REVERT: B  303 TRP cc_start: 0.8489 (m-10) cc_final: 0.8044 (m100)
REVERT: B  391 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8619 (pp)
REVERT: B  422 GLU cc_start: 0.8441 (pm20) cc_final: 0.8234 (pm20)
REVERT: B  436 HIS cc_start: 0.7953 (m-70) cc_final: 0.7569 (m-70)
REVERT: B  571 GLN cc_start: 0.8311 (tt0) cc_final: 0.7735 (tp40)
REVERT: A  178 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7999 (t80)
REVERT: A  209 MET cc_start: 0.8886 (tmt) cc_final: 0.8413 (tmm)
REVERT: A  302 TYR cc_start: 0.9146 (t80) cc_final: 0.8381 (t80)
REVERT: A  303 TRP cc_start: 0.8482 (m-10) cc_final: 0.8086 (m100)
REVERT: A  368 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9093 (mm)
REVERT: A  391 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8507 (pp)
REVERT: A  571 GLN cc_start: 0.8315 (tt0) cc_final: 0.7760 (tp40)
  outliers start: 32
  outliers final: 20
  residues processed: 149
  average time/residue: 0.0553
  time to fit residues: 12.6771
Evaluate side-chains
  148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  173 LEU
Chi-restraints excluded: chain B residue  191 ILE
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  278 CYS
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  385 PHE
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  429 ASP
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain B residue  505 LEU
Chi-restraints excluded: chain B residue  513 ASP
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  194 MET
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  385 PHE
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  410 MET
Chi-restraints excluded: chain A residue  429 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  557 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 36 optimal weight:    0.4980
   chunk 86 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.110824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.092774 restraints weight = 14378.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.096438 restraints weight = 6682.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.098913 restraints weight = 4006.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.100246 restraints weight = 2805.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.101650 restraints weight = 2253.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7410  Z= 0.142
  Angle     :  0.729  12.796  10084  Z= 0.354
  Chirality :  0.043   0.184   1178
  Planarity :  0.005   0.054   1234
  Dihedral  :  4.633  23.788    986
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 23.18 %
    Favored  : 72.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.29), residues: 930
  helix:  1.75 (0.21), residues: 666
  sheet:  None (None), residues: 0
  loop : -3.05 (0.35), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 334 
 TYR   0.013   0.001   TYR B 524 
 PHE   0.029   0.002   PHE B 174 
 TRP   0.012   0.001   TRP A 469 
 HIS   0.007   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7410)
  covalent geometry    : angle       0.72923 (10084)
  hydrogen bonds       : bond        0.04006 (  486)
  hydrogen bonds       : angle       3.60610 ( 1422)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1093.07 seconds
wall clock time: 19 minutes 34.59 seconds (1174.59 seconds total)