Starting phenix.real_space_refine
on Fri Aug 22 20:27:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cqb_16794/08_2025/8cqb_16794.cif"
  }
  resolution = 3.7
  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=   0.043
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: 8
    Type Number    sf(0)   Gaussians
     Al      2      5.89       5
     P       4      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    4860      2.51       5
     N    1292      2.21       5
     O    1486      1.98       5
     F       6      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7688
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3811
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 20, 'TRANS': 457}
    Chain: "B"
      Number of atoms: 3811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3811
          Classifications: {'peptide': 478}
          Link IDs: {'PTRANS': 20, 'TRANS': 457}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'AF3': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'AF3': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.12, per 1000 atoms: 0.28
  Number of scatterers: 7688
  At special positions: 0
  Unit cell: (70.89, 95.076, 150.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      36     16.00
     P       4     15.00
     Al      2     13.00
     Mg      2     11.99
     F       6      9.00
     O    1486      8.00
     N    1292      7.00
     C    4860      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.72
  Conformation dependent library (CDL) restraints added in 494.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1816

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      57.5% alpha, 9.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 33
      removed outlier: 3.795A  pdb=" N   ILE A  30 " --> pdb=" O   GLU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 60
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.717A  pdb=" N   ASP A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 154
    Processing helix  chain 'A' and resid 170 through 174
      removed outlier: 3.924A  pdb=" N   SER A 173 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 206
    Processing helix  chain 'A' and resid 213 through 230
      removed outlier: 3.539A  pdb=" N   GLU A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      Proline residue:  A 222  - end of helix
    Processing helix  chain 'A' and resid 249 through 253
    Processing helix  chain 'A' and resid 259 through 277
      removed outlier: 3.524A  pdb=" N   VAL A 263 " --> pdb=" O   ASP A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 305
    Processing helix  chain 'A' and resid 315 through 322
      removed outlier: 3.515A  pdb=" N   LEU A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 342
    Processing helix  chain 'A' and resid 350 through 372
    Processing helix  chain 'A' and resid 375 through 377
      No H-bonds generated for 'chain 'A' and resid 375 through 377'
    Processing helix  chain 'A' and resid 378 through 424
      Proline residue:  A 417  - end of helix
    Processing helix  chain 'A' and resid 432 through 450
      removed outlier: 4.046A  pdb=" N   PHE A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 4.828A  pdb=" N   GLN A 438 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 5.088A  pdb=" N   GLN A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 468
    Processing helix  chain 'A' and resid 469 through 483
      removed outlier: 3.784A  pdb=" N   ALA A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   ILE A 475 " --> pdb=" O   MET A 471 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 32
      removed outlier: 3.629A  pdb=" N   ILE B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 3.580A  pdb=" N   LYS B  57 " --> pdb=" O   TYR B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 123
      removed outlier: 3.693A  pdb=" N   ASP B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 155
      removed outlier: 3.606A  pdb=" N   GLU B 147 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS B 155 " --> pdb=" O   ARG B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 174
      removed outlier: 3.757A  pdb=" N   SER B 173 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 206
    Processing helix  chain 'B' and resid 213 through 230
      Proline residue:  B 222  - end of helix
    Processing helix  chain 'B' and resid 259 through 277
    Processing helix  chain 'B' and resid 289 through 305
    Processing helix  chain 'B' and resid 316 through 341
    Processing helix  chain 'B' and resid 349 through 372
      removed outlier: 5.117A  pdb=" N   GLU B 366 " --> pdb=" O   ARG B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 377
      No H-bonds generated for 'chain 'B' and resid 375 through 377'
    Processing helix  chain 'B' and resid 378 through 415
    Processing helix  chain 'B' and resid 415 through 420
    Processing helix  chain 'B' and resid 425 through 429
      removed outlier: 3.538A  pdb=" N   LYS B 429 " --> pdb=" O   ILE B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 431 through 448
      removed outlier: 3.769A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLN B 438 " --> pdb=" O   ARG B 434 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ASP B 442 " --> pdb=" O   GLN B 438 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   LYS B 445 " --> pdb=" O   GLN B 441 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   LYS B 446 " --> pdb=" O   ASP B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 456
      No H-bonds generated for 'chain 'B' and resid 454 through 456'
    Processing helix  chain 'B' and resid 457 through 473
      removed outlier: 3.671A  pdb=" N   LEU B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLN B 462 " --> pdb=" O   GLU B 458 " (cutoff:3.500A)
      removed outlier: 5.963A  pdb=" N   SER B 470 " --> pdb=" O   LYS B 466 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   MET B 471 " --> pdb=" O   SER B 467 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   ASP B 473 " --> pdb=" O   GLU B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 483
      removed outlier: 3.741A  pdb=" N   LEU B 482 " --> pdb=" O   THR B 478 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 6.922A  pdb=" N   ILE A  78 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL A  39 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU A  96 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 7.824A  pdb=" N   THR A  98 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   ILE A  43 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   PHE A 178 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   PHE A 236 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   TRP A 180 " --> pdb=" O   PHE A 236 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 23
      removed outlier: 3.658A  pdb=" N   MET B  22 " --> pdb=" O   GLU B  15 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE B  78 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  94 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   LEU B  96 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   VAL B  41 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 8.149A  pdb=" N   THR B  98 " --> pdb=" O   VAL B  41 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 45
      removed outlier: 8.486A  pdb=" N   PHE B 236 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   TRP B 180 " --> pdb=" O   PHE B 236 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 191

    418 hydrogen bonds defined for protein.
    1215 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: 1.11

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2514
        1.34 -     1.46: 1582
        1.46 -     1.58: 3673
        1.58 -     1.69: 3
        1.69 -     1.81: 62
  Bond restraints: 7834
  Sorted by residual:
  bond pdb=" F3  AF3 A 602 "
       pdb="AL   AF3 A 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.708 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" F1  AF3 A 602 "
       pdb="AL   AF3 A 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.708 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" F3  AF3 B 602 "
       pdb="AL   AF3 B 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.707 -0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" F2  AF3 A 602 "
       pdb="AL   AF3 A 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.706 -0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" F1  AF3 B 602 "
       pdb="AL   AF3 B 602 "
    ideal  model  delta    sigma   weight residual
    1.637  1.706 -0.069 2.00e-02 2.50e+03 1.18e+01
  ... (remaining 7829 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 10432
        2.14 -     4.28: 126
        4.28 -     6.42: 23
        6.42 -     8.56: 4
        8.56 -    10.71: 5
  Bond angle restraints: 10590
  Sorted by residual:
  angle pdb=" O5' GDP A 601 "
        pdb=" PA  GDP A 601 "
        pdb=" O2A GDP A 601 "
      ideal   model   delta    sigma   weight residual
     109.50   98.79   10.71 3.00e+00 1.11e-01 1.27e+01
  angle pdb=" C   LYS A 209 "
        pdb=" N   LYS A 210 "
        pdb=" CA  LYS A 210 "
      ideal   model   delta    sigma   weight residual
     121.54  128.21   -6.67 1.91e+00 2.74e-01 1.22e+01
  angle pdb=" C3' GDP A 601 "
        pdb=" C2' GDP A 601 "
        pdb=" C1' GDP A 601 "
      ideal   model   delta    sigma   weight residual
     111.00  100.58   10.42 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" C   LYS B 209 "
        pdb=" N   LYS B 210 "
        pdb=" CA  LYS B 210 "
      ideal   model   delta    sigma   weight residual
     121.54  127.96   -6.42 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" O3A GDP A 601 "
        pdb=" PB  GDP A 601 "
        pdb=" O3B GDP A 601 "
      ideal   model   delta    sigma   weight residual
     109.50  100.17    9.33 3.00e+00 1.11e-01 9.67e+00
  ... (remaining 10585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.80: 4310
       24.80 -    49.61: 409
       49.61 -    74.41: 51
       74.41 -    99.21: 16
       99.21 -   124.01: 2
  Dihedral angle restraints: 4788
    sinusoidal: 1988
      harmonic: 2800
  Sorted by residual:
  dihedral pdb=" O2B GDP A 601 "
           pdb=" O3A GDP A 601 "
           pdb=" PB  GDP A 601 "
           pdb=" PA  GDP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -55.99 -124.01     1      2.00e+01 2.50e-03 3.74e+01
  dihedral pdb=" O2B GDP B 601 "
           pdb=" O3A GDP B 601 "
           pdb=" PB  GDP B 601 "
           pdb=" PA  GDP B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -78.27 -101.73     1      2.00e+01 2.50e-03 2.89e+01
  dihedral pdb=" O4' GDP A 601 "
           pdb=" C1' GDP A 601 "
           pdb=" N9  GDP A 601 "
           pdb=" C8  GDP A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      27.02  119.09  -92.07     1      2.00e+01 2.50e-03 2.49e+01
  ... (remaining 4785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 746
       0.028 -    0.055: 272
       0.055 -    0.083: 83
       0.083 -    0.110: 64
       0.110 -    0.138: 17
  Chirality restraints: 1182
  Sorted by residual:
  chirality pdb=" C3' GDP A 601 "
            pdb=" C4' GDP A 601 "
            pdb=" O3' GDP A 601 "
            pdb=" C2' GDP A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.65    0.14 2.00e-01 2.50e+01 4.75e-01
  chirality pdb=" CA  LYS A 210 "
            pdb=" N   LYS A 210 "
            pdb=" C   LYS A 210 "
            pdb=" CB  LYS A 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  VAL B 179 "
            pdb=" N   VAL B 179 "
            pdb=" C   VAL B 179 "
            pdb=" CB  VAL B 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 1179 not shown)

  Planarity restraints: 1358
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 197 "   -0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO B 198 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 198 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 198 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 230 "   -0.028 5.00e-02 4.00e+02   4.30e-02 2.96e+00
        pdb=" N   PRO B 231 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 231 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 231 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  36 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.54e+00
        pdb=" N   PRO B  37 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B  37 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  37 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1355 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.93: 3
        1.93 -     2.68: 174
        2.68 -     3.42: 11489
        3.42 -     4.16: 18100
        4.16 -     4.90: 32865
  Nonbonded interactions: 62631
  Sorted by model distance:
  nonbonded pdb=" O2B GDP A 601 "
            pdb="MG    MG A 603 "
     model   vdw
     1.193 2.170
  nonbonded pdb=" O1B GDP A 601 "
            pdb=" F2  AF3 A 602 "
     model   vdw
     1.892 2.990
  nonbonded pdb=" O3B GDP B 601 "
            pdb=" F3  AF3 B 602 "
     model   vdw
     1.912 2.990
  nonbonded pdb=" OG1 THR B  75 "
            pdb="MG    MG B 603 "
     model   vdw
     1.952 2.170
  nonbonded pdb=" OG  SER B  52 "
            pdb="MG    MG B 603 "
     model   vdw
     1.953 2.170
  ... (remaining 62626 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     9.030
  Find NCS groups from input model:        0.090
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
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      :  0.003   0.071   7835  Z= 0.167
  Angle     :  0.635  10.705  10590  Z= 0.304
  Chirality :  0.039   0.138   1182
  Planarity :  0.004   0.048   1358
  Dihedral  : 18.673 124.013   2972
  Min Nonbonded Distance : 1.193

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.09 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 24.53 %
    Favored  : 74.18 %
  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 aren not related in a simple way.
  whole: -0.44 (0.27), residues: 952
  helix:  0.64 (0.23), residues: 494
  sheet:  0.62 (0.47), residues: 98
  loop : -1.88 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 245 
 TYR   0.015   0.001   TYR B  47 
 PHE   0.014   0.001   PHE A 219 
 TRP   0.005   0.001   TRP A 114 
 HIS   0.005   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7834)
  covalent geometry    : angle       0.63536 (10590)
  hydrogen bonds       : bond        0.14625 (  418)
  hydrogen bonds       : angle       6.09991 ( 1215)
  Misc. bond           : bond        0.00032 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  471 MET cc_start: 0.7641 (ppp) cc_final: 0.6989 (ppp)
REVERT: B  334 HIS cc_start: 0.8128 (t70) cc_final: 0.7839 (t70)
REVERT: B  358 ARG cc_start: 0.7899 (tpm170) cc_final: 0.7617 (tpm170)
  outliers start: 11
  outliers final: 2
  residues processed: 126
  average time/residue: 0.1189
  time to fit residues: 19.5035
Evaluate side-chains
  97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   70 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 111 ASN
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 357 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.179281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.143474 restraints weight = 10575.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.147841 restraints weight = 15470.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.148695 restraints weight = 9764.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.151822 restraints weight = 6613.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.152300 restraints weight = 5361.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.1355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   7835  Z= 0.215
  Angle     :  0.705   9.856  10590  Z= 0.347
  Chirality :  0.044   0.182   1182
  Planarity :  0.005   0.049   1358
  Dihedral  :  9.375 131.154   1044
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.72 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 26.06 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.27), residues: 952
  helix:  0.80 (0.23), residues: 498
  sheet:  0.31 (0.47), residues: 98
  loop : -2.02 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 452 
 TYR   0.019   0.002   TYR B  47 
 PHE   0.019   0.002   PHE A 373 
 TRP   0.006   0.001   TRP B 114 
 HIS   0.007   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 7834)
  covalent geometry    : angle       0.70519 (10590)
  hydrogen bonds       : bond        0.04543 (  418)
  hydrogen bonds       : angle       4.86150 ( 1215)
  Misc. bond           : bond        0.00080 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.6169 (t80) cc_final: 0.5441 (t80)
REVERT: B  112 ASP cc_start: 0.6963 (t0) cc_final: 0.6545 (t0)
REVERT: B  162 GLU cc_start: -0.1367 (OUTLIER) cc_final: -0.3858 (mm-30)
REVERT: B  334 HIS cc_start: 0.7972 (t70) cc_final: 0.7733 (t70)
REVERT: B  368 PHE cc_start: 0.7790 (t80) cc_final: 0.7513 (t80)
  outliers start: 17
  outliers final: 10
  residues processed: 124
  average time/residue: 0.1041
  time to fit residues: 17.1285
Evaluate side-chains
  107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  131 ILE
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 87 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:   20.0000
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
B  16 ASN
B 276 ASN
B 302 ASN
B 378 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.180186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.132064 restraints weight = 10519.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.136063 restraints weight = 8143.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.136587 restraints weight = 6559.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.137925 restraints weight = 5997.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.138528 restraints weight = 5528.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7835  Z= 0.160
  Angle     :  0.652   9.601  10590  Z= 0.321
  Chirality :  0.042   0.192   1182
  Planarity :  0.004   0.049   1358
  Dihedral  :  8.961 135.300   1043
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.09 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 25.94 %
    Favored  : 70.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.27), residues: 952
  helix:  1.02 (0.23), residues: 493
  sheet:  0.27 (0.46), residues: 98
  loop : -2.03 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 151 
 TYR   0.018   0.002   TYR B  47 
 PHE   0.016   0.002   PHE A 116 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.009   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 7834)
  covalent geometry    : angle       0.65158 (10590)
  hydrogen bonds       : bond        0.04072 (  418)
  hydrogen bonds       : angle       4.62237 ( 1215)
  Misc. bond           : bond        0.00025 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.6103 (t80) cc_final: 0.5333 (t80)
REVERT: B  101 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7990 (mt)
REVERT: B  112 ASP cc_start: 0.7078 (t0) cc_final: 0.6767 (t0)
REVERT: B  139 MET cc_start: 0.7838 (mmt) cc_final: 0.7379 (tpp)
REVERT: B  162 GLU cc_start: -0.1262 (OUTLIER) cc_final: -0.3934 (mm-30)
REVERT: B  334 HIS cc_start: 0.8143 (t70) cc_final: 0.7833 (t70)
  outliers start: 27
  outliers final: 9
  residues processed: 126
  average time/residue: 0.1114
  time to fit residues: 18.4154
Evaluate side-chains
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0770
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.9542

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

Flipped N/Q/H residues before XYZ refinement:
A 254 GLN
B  16 ASN
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.179559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.131891 restraints weight = 10566.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135095 restraints weight = 7769.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.137253 restraints weight = 6322.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.138335 restraints weight = 5536.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139662 restraints weight = 5101.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   7835  Z= 0.159
  Angle     :  0.659   9.493  10590  Z= 0.325
  Chirality :  0.042   0.164   1182
  Planarity :  0.004   0.049   1358
  Dihedral  :  8.879 130.653   1042
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.41 %
    Favored  : 93.17 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 26.64 %
    Favored  : 70.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.27), residues: 952
  helix:  1.05 (0.23), residues: 494
  sheet:  0.24 (0.47), residues: 98
  loop : -1.98 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 358 
 TYR   0.015   0.002   TYR B  47 
 PHE   0.016   0.002   PHE B 436 
 TRP   0.004   0.001   TRP A  79 
 HIS   0.009   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 7834)
  covalent geometry    : angle       0.65857 (10590)
  hydrogen bonds       : bond        0.03972 (  418)
  hydrogen bonds       : angle       4.56324 ( 1215)
  Misc. bond           : bond        0.00029 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.6224 (t80) cc_final: 0.5387 (t80)
REVERT: B    8 THR cc_start: 0.5127 (OUTLIER) cc_final: 0.4678 (t)
REVERT: B  101 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7955 (mt)
REVERT: B  112 ASP cc_start: 0.7081 (t0) cc_final: 0.6817 (t0)
REVERT: B  139 MET cc_start: 0.7926 (mmt) cc_final: 0.7460 (tpp)
REVERT: B  334 HIS cc_start: 0.8030 (t70) cc_final: 0.7792 (t70)
  outliers start: 22
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1191
  time to fit residues: 17.7107
Evaluate side-chains
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  270 CYS
Chi-restraints excluded: chain B residue    8 THR
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 78 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 30 optimal weight:    9.9990
   chunk 79 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 161 ASN
B  16 ASN
B 161 ASN
** B 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 378 HIS
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.180963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.135099 restraints weight = 10851.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.135002 restraints weight = 8713.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.135150 restraints weight = 9136.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.135901 restraints weight = 7843.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.136033 restraints weight = 7429.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080   7835  Z= 0.441
  Angle     :  0.952  14.063  10590  Z= 0.474
  Chirality :  0.053   0.253   1182
  Planarity :  0.007   0.098   1358
  Dihedral  : 10.354 135.192   1042
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 19.75
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.51 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 25.47 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.26), residues: 952
  helix:  0.20 (0.22), residues: 499
  sheet: -1.54 (0.50), residues: 97
  loop : -2.41 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 370 
 TYR   0.030   0.003   TYR A  47 
 PHE   0.036   0.004   PHE B 126 
 TRP   0.007   0.002   TRP B  79 
 HIS   0.007   0.002   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.01010 ( 7834)
  covalent geometry    : angle       0.95165 (10590)
  hydrogen bonds       : bond        0.06085 (  418)
  hydrogen bonds       : angle       5.64330 ( 1215)
  Misc. bond           : bond        0.00238 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 92
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7954 (mmp-170)
REVERT: A  161 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5504 (t0)
REVERT: A  216 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.7165 (m-30)
REVERT: A  229 PHE cc_start: 0.6595 (t80) cc_final: 0.5603 (t80)
REVERT: B   88 LYS cc_start: 0.6182 (tttt) cc_final: 0.5643 (tmtt)
REVERT: B  101 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8183 (mt)
REVERT: B  161 ASN cc_start: 0.2406 (OUTLIER) cc_final: 0.2199 (t0)
REVERT: B  229 PHE cc_start: 0.7200 (t80) cc_final: 0.6943 (t80)
REVERT: B  334 HIS cc_start: 0.8101 (t70) cc_final: 0.7891 (t70)
  outliers start: 45
  outliers final: 19
  residues processed: 130
  average time/residue: 0.1126
  time to fit residues: 19.1063
Evaluate side-chains
  109 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue   48 ARG
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   70 THR
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  161 ASN
Chi-restraints excluded: chain A residue  216 ASP
Chi-restraints excluded: chain A residue  221 LEU
Chi-restraints excluded: chain A residue  244 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  455 ILE
Chi-restraints excluded: chain B residue   22 MET
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  101 LEU
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  161 ASN
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  460 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 59 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 161 ASN
B 334 HIS
B 338 GLN
B 400 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.189717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.141781 restraints weight = 10547.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.146966 restraints weight = 8021.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.146809 restraints weight = 6494.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.148439 restraints weight = 5885.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.149157 restraints weight = 5408.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   7835  Z= 0.156
  Angle     :  0.708  10.110  10590  Z= 0.349
  Chirality :  0.044   0.230   1182
  Planarity :  0.004   0.052   1358
  Dihedral  :  9.264 117.058   1042
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  5.99 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 27.46 %
    Favored  : 69.01 %
  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 aren not related in a simple way.
  whole: -0.74 (0.27), residues: 952
  helix:  0.75 (0.23), residues: 491
  sheet: -1.04 (0.51), residues: 97
  loop : -2.07 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 370 
 TYR   0.032   0.002   TYR A  47 
 PHE   0.017   0.002   PHE A 116 
 TRP   0.005   0.001   TRP A 114 
 HIS   0.007   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 7834)
  covalent geometry    : angle       0.70753 (10590)
  hydrogen bonds       : bond        0.04185 (  418)
  hydrogen bonds       : angle       4.88095 ( 1215)
  Misc. bond           : bond        0.00025 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 ARG cc_start: 0.6155 (tpp80) cc_final: 0.5873 (tpp80)
REVERT: A  229 PHE cc_start: 0.6531 (t80) cc_final: 0.5639 (t80)
REVERT: B  139 MET cc_start: 0.8070 (mmt) cc_final: 0.7550 (tpp)
REVERT: B  229 PHE cc_start: 0.7056 (t80) cc_final: 0.6767 (t80)
  outliers start: 30
  outliers final: 18
  residues processed: 128
  average time/residue: 0.1124
  time to fit residues: 18.6790
Evaluate side-chains
  108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  289 ASN
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain B residue   22 MET
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 56 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0870
   chunk 6 optimal weight:    0.0170
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN
B  16 ASN
B 334 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.179468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132182 restraints weight = 10492.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.134928 restraints weight = 7856.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.136587 restraints weight = 6485.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.138353 restraints weight = 5755.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.138895 restraints weight = 5250.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7835  Z= 0.132
  Angle     :  0.691  10.612  10590  Z= 0.339
  Chirality :  0.044   0.243   1182
  Planarity :  0.004   0.047   1358
  Dihedral  :  8.739 110.296   1042
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.30 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 28.40 %
    Favored  : 68.66 %
  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 aren not related in a simple way.
  whole: -0.42 (0.28), residues: 952
  helix:  0.96 (0.23), residues: 495
  sheet: -0.57 (0.50), residues: 97
  loop : -1.97 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 153 
 TYR   0.026   0.002   TYR A  47 
 PHE   0.020   0.002   PHE A 373 
 TRP   0.006   0.001   TRP A 114 
 HIS   0.007   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7834)
  covalent geometry    : angle       0.69102 (10590)
  hydrogen bonds       : bond        0.03899 (  418)
  hydrogen bonds       : angle       4.58751 ( 1215)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8524 (pmm) cc_final: 0.8293 (pmm)
REVERT: A  229 PHE cc_start: 0.6630 (t80) cc_final: 0.5670 (t80)
REVERT: B  139 MET cc_start: 0.7998 (mmt) cc_final: 0.7500 (tpp)
REVERT: B  229 PHE cc_start: 0.7076 (t80) cc_final: 0.6728 (t80)
REVERT: B  322 ILE cc_start: 0.6811 (mm) cc_final: 0.6377 (mm)
REVERT: B  334 HIS cc_start: 0.7986 (t70) cc_final: 0.7717 (t-90)
REVERT: B  338 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8274 (mp10)
  outliers start: 25
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1007
  time to fit residues: 15.5110
Evaluate side-chains
  105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  321 GLN
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Chi-restraints excluded: chain B residue  470 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0030
   chunk 76 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0270
   chunk 4 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 66 optimal weight:    0.4980
   overall best weight:    0.3848

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.182263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.134393 restraints weight = 10512.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.137513 restraints weight = 7803.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139047 restraints weight = 6381.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.141137 restraints weight = 5648.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.142084 restraints weight = 5131.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.3261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7835  Z= 0.125
  Angle     :  0.680  10.801  10590  Z= 0.332
  Chirality :  0.042   0.162   1182
  Planarity :  0.004   0.048   1358
  Dihedral  :  8.317 104.473   1042
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.09 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 29.23 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.28), residues: 952
  helix:  1.16 (0.24), residues: 491
  sheet: -0.26 (0.51), residues: 94
  loop : -1.92 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 153 
 TYR   0.023   0.002   TYR A  47 
 PHE   0.026   0.002   PHE A 368 
 TRP   0.006   0.001   TRP A 114 
 HIS   0.017   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7834)
  covalent geometry    : angle       0.68042 (10590)
  hydrogen bonds       : bond        0.03653 (  418)
  hydrogen bonds       : angle       4.50365 ( 1215)
  Misc. bond           : bond        0.00017 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8519 (pmm) cc_final: 0.8273 (pmm)
REVERT: A  401 GLU cc_start: 0.7818 (tp30) cc_final: 0.7605 (tp30)
REVERT: B   55 MET cc_start: 0.7615 (mmm) cc_final: 0.7372 (mmm)
REVERT: B  139 MET cc_start: 0.8005 (mmt) cc_final: 0.7509 (tpp)
REVERT: B  229 PHE cc_start: 0.7156 (t80) cc_final: 0.6836 (t80)
REVERT: B  322 ILE cc_start: 0.6783 (mm) cc_final: 0.6327 (mm)
REVERT: B  334 HIS cc_start: 0.8046 (t70) cc_final: 0.7826 (t70)
REVERT: B  339 MET cc_start: 0.7589 (mmt) cc_final: 0.7313 (mmm)
  outliers start: 20
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1003
  time to fit residues: 15.8419
Evaluate side-chains
  102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 93 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  16 ASN
B 378 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.179548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131462 restraints weight = 10604.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.133806 restraints weight = 8601.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.136478 restraints weight = 7064.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.137346 restraints weight = 6233.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.137614 restraints weight = 5550.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7835  Z= 0.158
  Angle     :  0.717  10.745  10590  Z= 0.348
  Chirality :  0.044   0.280   1182
  Planarity :  0.005   0.074   1358
  Dihedral  :  8.548 115.198   1042
  Min Nonbonded Distance : 1.892

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.51 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 29.34 %
    Favored  : 68.66 %
  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 aren not related in a simple way.
  whole: -0.21 (0.28), residues: 952
  helix:  1.12 (0.24), residues: 492
  sheet: -0.39 (0.50), residues: 97
  loop : -1.86 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 153 
 TYR   0.031   0.002   TYR A  47 
 PHE   0.020   0.002   PHE A 373 
 TRP   0.008   0.001   TRP B 114 
 HIS   0.012   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7834)
  covalent geometry    : angle       0.71740 (10590)
  hydrogen bonds       : bond        0.03875 (  418)
  hydrogen bonds       : angle       4.56532 ( 1215)
  Misc. bond           : bond        0.00010 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8506 (pmm) cc_final: 0.8188 (pmm)
REVERT: A  229 PHE cc_start: 0.6663 (t80) cc_final: 0.5642 (t80)
REVERT: A  458 GLU cc_start: 0.7646 (pm20) cc_final: 0.7365 (mm-30)
REVERT: B   55 MET cc_start: 0.7685 (mmm) cc_final: 0.7305 (mmm)
REVERT: B  139 MET cc_start: 0.8021 (mmt) cc_final: 0.7559 (tpp)
REVERT: B  229 PHE cc_start: 0.7184 (t80) cc_final: 0.6870 (t80)
REVERT: B  322 ILE cc_start: 0.6955 (mm) cc_final: 0.6488 (mm)
REVERT: B  334 HIS cc_start: 0.8080 (t70) cc_final: 0.7759 (t-170)
  outliers start: 17
  outliers final: 14
  residues processed: 97
  average time/residue: 0.1116
  time to fit residues: 14.3332
Evaluate side-chains
  93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  378 HIS
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 56 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.179328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.131883 restraints weight = 10497.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.134554 restraints weight = 8274.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.136067 restraints weight = 6594.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.136655 restraints weight = 6034.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.137167 restraints weight = 5887.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7835  Z= 0.153
  Angle     :  0.716  10.951  10590  Z= 0.348
  Chirality :  0.044   0.297   1182
  Planarity :  0.004   0.048   1358
  Dihedral  :  8.490 115.367   1042
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.93 %
    Favored  : 92.65 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 29.58 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.28), residues: 952
  helix:  1.11 (0.23), residues: 492
  sheet: -0.42 (0.50), residues: 97
  loop : -1.90 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 153 
 TYR   0.028   0.002   TYR A  47 
 PHE   0.028   0.002   PHE A 368 
 TRP   0.007   0.001   TRP B 114 
 HIS   0.012   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 7834)
  covalent geometry    : angle       0.71646 (10590)
  hydrogen bonds       : bond        0.03854 (  418)
  hydrogen bonds       : angle       4.52265 ( 1215)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1904 Ramachandran restraints generated.
    952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   11 MET cc_start: 0.8506 (pmm) cc_final: 0.8183 (pmm)
REVERT: A  229 PHE cc_start: 0.6657 (t80) cc_final: 0.5650 (t80)
REVERT: A  253 LEU cc_start: 0.7281 (mt) cc_final: 0.7073 (mt)
REVERT: A  458 GLU cc_start: 0.7610 (pm20) cc_final: 0.7364 (mm-30)
REVERT: B   55 MET cc_start: 0.7663 (mmm) cc_final: 0.7312 (mmm)
REVERT: B  139 MET cc_start: 0.8030 (mmt) cc_final: 0.7584 (tpp)
REVERT: B  229 PHE cc_start: 0.7118 (t80) cc_final: 0.6780 (t80)
REVERT: B  322 ILE cc_start: 0.6933 (mm) cc_final: 0.6469 (mm)
REVERT: B  334 HIS cc_start: 0.8103 (t70) cc_final: 0.7769 (t-170)
  outliers start: 14
  outliers final: 14
  residues processed: 96
  average time/residue: 0.0994
  time to fit residues: 12.9569
Evaluate side-chains
  96 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ILE
Chi-restraints excluded: chain A residue   44 VAL
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  134 ILE
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  204 TYR
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  437 VAL
Chi-restraints excluded: chain B residue  438 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 17 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   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 378 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.181076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.132952 restraints weight = 10492.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.135843 restraints weight = 7873.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.137919 restraints weight = 6536.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.139144 restraints weight = 5772.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.139591 restraints weight = 5323.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7835  Z= 0.138
  Angle     :  0.705  10.930  10590  Z= 0.342
  Chirality :  0.043   0.267   1182
  Planarity :  0.004   0.048   1358
  Dihedral  :  8.250 112.095   1042
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  6.62 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 29.58 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.28), residues: 952
  helix:  1.15 (0.23), residues: 493
  sheet: -0.33 (0.50), residues: 97
  loop : -1.89 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 153 
 TYR   0.027   0.002   TYR A  47 
 PHE   0.019   0.001   PHE A 373 
 TRP   0.007   0.001   TRP B 114 
 HIS   0.012   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7834)
  covalent geometry    : angle       0.70519 (10590)
  hydrogen bonds       : bond        0.03678 (  418)
  hydrogen bonds       : angle       4.46660 ( 1215)
  Misc. bond           : bond        0.00004 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1583.96 seconds
wall clock time: 28 minutes 14.57 seconds (1694.57 seconds total)