Starting phenix.real_space_refine
on Wed Sep 17 13:04:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ria_19185/09_2025/8ria_19185.cif"
  }
  resolution = 4.4
  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=   0.002 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5642      2.51       5
     N    1464      2.21       5
     O    1644      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8786
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4393
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 17, 'TRANS': 553}
    Chain: "B"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 571, 4393
          Classifications: {'peptide': 571}
          Link IDs: {'PTRANS': 17, 'TRANS': 553}
  Time building chain proxies: 2.22, per 1000 atoms: 0.25
  Number of scatterers: 8786
  At special positions: 0
  Unit cell: (75.57, 108.775, 135.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1644      8.00
     N    1464      7.00
     C    5642      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 349.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2100

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 6 sheets defined
      69.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
    Processing helix  chain 'A' and resid 25 through 55
      Proline residue:  A  47  - end of helix
      removed outlier: 3.806A  pdb=" N   THR A  50 " --> pdb=" O   ILE A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 110
      removed outlier: 3.610A  pdb=" N   THR A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 119
      removed outlier: 3.924A  pdb=" N   ASP A 116 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ALA A 119 " --> pdb=" O   PHE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 163
      removed outlier: 3.788A  pdb=" N   VAL A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 143 " --> pdb=" O   THR A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 210
      Proline residue:  A 175  - end of helix
      Proline residue:  A 183  - end of helix
    Processing helix  chain 'A' and resid 211 through 220
    Processing helix  chain 'A' and resid 221 through 276
      Proline residue:  A 252  - end of helix
    Processing helix  chain 'A' and resid 281 through 323
      removed outlier: 3.580A  pdb=" N   LEU A 288 " --> pdb=" O   VAL A 284 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 4.156A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 307 " --> pdb=" O   PHE A 303 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   GLN A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 323 " --> pdb=" O   GLU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 409 through 417
      removed outlier: 3.506A  pdb=" N   TRP A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 438
      removed outlier: 4.317A  pdb=" N   ASN A 434 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 455
    Processing helix  chain 'A' and resid 458 through 464
      removed outlier: 3.655A  pdb=" N   LEU A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 511 through 525
    Processing helix  chain 'A' and resid 537 through 542
    Processing helix  chain 'A' and resid 560 through 567
    Processing helix  chain 'A' and resid 571 through 580
    Processing helix  chain 'B' and resid 11 through 22
    Processing helix  chain 'B' and resid 25 through 57
      removed outlier: 3.752A  pdb=" N   LEU B  29 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA B  30 " --> pdb=" O   TYR B  26 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
      removed outlier: 3.537A  pdb=" N   THR B  50 " --> pdb=" O   ILE B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 60 through 110
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 4.394A  pdb=" N   ASP B 116 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 163
      removed outlier: 3.954A  pdb=" N   VAL B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER B 143 " --> pdb=" O   THR B 139 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ILE B 146 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 210
      Proline residue:  B 175  - end of helix
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 221 through 275
      Proline residue:  B 252  - end of helix
    Processing helix  chain 'B' and resid 279 through 295
      removed outlier: 3.741A  pdb=" N   VAL B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 323
      removed outlier: 4.551A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LYS B 309 " --> pdb=" O   THR B 305 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   GLU B 323 " --> pdb=" O   GLU B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 388
    Processing helix  chain 'B' and resid 409 through 416
    Processing helix  chain 'B' and resid 431 through 438
      removed outlier: 4.202A  pdb=" N   ILE B 435 " --> pdb=" O   ILE B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
    Processing helix  chain 'B' and resid 456 through 461
      removed outlier: 3.853A  pdb=" N   PHE B 460 " --> pdb=" O   TYR B 456 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ILE B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 456 through 461'
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.535A  pdb=" N   ASN B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 524
    Processing helix  chain 'B' and resid 536 through 543
      removed outlier: 3.950A  pdb=" N   VAL B 540 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 562 through 571
      removed outlier: 3.681A  pdb=" N   ARG B 571 " --> pdb=" O   HIS B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 364
      removed outlier: 7.519A  pdb=" N   ALA A 362 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   ASP A 344 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   ILE A 364 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   GLN A 342 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA3, first strand: chain 'A' and resid 499 through 502
      removed outlier: 3.505A  pdb=" N   ILE A 531 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 360 through 364
      removed outlier: 7.396A  pdb=" N   ALA B 362 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ASP B 344 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   ILE B 364 " --> pdb=" O   GLN B 342 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   GLN B 342 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 499 through 502
      removed outlier: 6.470A  pdb=" N   THR B 370 " --> pdb=" O   VAL B 532 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   PHE B 548 " --> pdb=" O   THR B 555 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 429 through 430

    610 hydrogen bonds defined for protein.
    1812 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: 1.42

  Time building geometry restraints manager: 1.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1953
        1.33 -     1.45: 1743
        1.45 -     1.57: 5153
        1.57 -     1.69: 1
        1.69 -     1.81: 70
  Bond restraints: 8920
  Sorted by residual:
  bond pdb=" N   PRO B 497 "
       pdb=" CD  PRO B 497 "
    ideal  model  delta    sigma   weight residual
    1.473  1.609 -0.136 1.40e-02 5.10e+03 9.45e+01
  bond pdb=" N   ASN B  23 "
       pdb=" CA  ASN B  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.41e-02 5.03e+03 9.37e+00
  bond pdb=" N   PRO B 465 "
       pdb=" CD  PRO B 465 "
    ideal  model  delta    sigma   weight residual
    1.473  1.508 -0.035 1.40e-02 5.10e+03 6.30e+00
  bond pdb=" CA  PRO A  24 "
       pdb=" C   PRO A  24 "
    ideal  model  delta    sigma   weight residual
    1.524  1.503  0.022 9.20e-03 1.18e+04 5.48e+00
  bond pdb=" CA  ASP B 116 "
       pdb=" C   ASP B 116 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 1.38e-02 5.25e+03 5.04e+00
  ... (remaining 8915 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.69: 11933
        7.69 -    15.38: 90
       15.38 -    23.08: 34
       23.08 -    30.77: 11
       30.77 -    38.46: 4
  Bond angle restraints: 12072
  Sorted by residual:
  angle pdb=" N   PHE B 460 "
        pdb=" CA  PHE B 460 "
        pdb=" C   PHE B 460 "
      ideal   model   delta    sigma   weight residual
     112.89  150.29  -37.40 1.24e+00 6.50e-01 9.10e+02
  angle pdb=" N   ASN A 163 "
        pdb=" CA  ASN A 163 "
        pdb=" C   ASN A 163 "
      ideal   model   delta    sigma   weight residual
     109.24   74.83   34.41 1.67e+00 3.59e-01 4.24e+02
  angle pdb=" N   PHE A  57 "
        pdb=" CA  PHE A  57 "
        pdb=" C   PHE A  57 "
      ideal   model   delta    sigma   weight residual
     113.31  151.77  -38.46 2.04e+00 2.40e-01 3.55e+02
  angle pdb=" C   THR B  22 "
        pdb=" CA  THR B  22 "
        pdb=" CB  THR B  22 "
      ideal   model   delta    sigma   weight residual
     111.68   81.16   30.52 1.67e+00 3.59e-01 3.34e+02
  angle pdb=" N   TRP A 164 "
        pdb=" CA  TRP A 164 "
        pdb=" C   TRP A 164 "
      ideal   model   delta    sigma   weight residual
     112.04  136.11  -24.07 1.44e+00 4.82e-01 2.79e+02
  ... (remaining 12067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 4787
       16.07 -    32.15: 512
       32.15 -    48.22: 82
       48.22 -    64.29: 9
       64.29 -    80.37: 8
  Dihedral angle restraints: 5398
    sinusoidal: 2128
      harmonic: 3270
  Sorted by residual:
  dihedral pdb=" C   THR B  22 "
           pdb=" N   THR B  22 "
           pdb=" CA  THR B  22 "
           pdb=" CB  THR B  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00  -81.86  -40.14     0      2.50e+00 1.60e-01 2.58e+02
  dihedral pdb=" C   ASP B 510 "
           pdb=" N   ASP B 510 "
           pdb=" CA  ASP B 510 "
           pdb=" CB  ASP B 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -156.44   33.84     0      2.50e+00 1.60e-01 1.83e+02
  dihedral pdb=" C   ASP A 510 "
           pdb=" N   ASP A 510 "
           pdb=" CA  ASP A 510 "
           pdb=" CB  ASP A 510 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.97   28.37     0      2.50e+00 1.60e-01 1.29e+02
  ... (remaining 5395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.283: 1426
       0.283 -    0.565: 21
       0.565 -    0.848: 7
       0.848 -    1.131: 3
       1.131 -    1.414: 5
  Chirality restraints: 1462
  Sorted by residual:
  chirality pdb=" CA  ASP B 510 "
            pdb=" N   ASP B 510 "
            pdb=" C   ASP B 510 "
            pdb=" CB  ASP B 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 5.00e+01
  chirality pdb=" CA  PHE A  57 "
            pdb=" N   PHE A  57 "
            pdb=" C   PHE A  57 "
            pdb=" CB  PHE A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.10    1.41 2.00e-01 2.50e+01 4.95e+01
  chirality pdb=" CA  ASP A 510 "
            pdb=" N   ASP A 510 "
            pdb=" C   ASP A 510 "
            pdb=" CB  ASP A 510 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.32    1.19 2.00e-01 2.50e+01 3.55e+01
  ... (remaining 1459 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 496 "    0.131 5.00e-02 4.00e+02   1.89e-01 5.74e+01
        pdb=" N   PRO B 497 "   -0.327 5.00e-02 4.00e+02
        pdb=" CA  PRO B 497 "    0.112 5.00e-02 4.00e+02
        pdb=" CD  PRO B 497 "    0.084 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 464 "   -0.065 5.00e-02 4.00e+02   9.77e-02 1.53e+01
        pdb=" N   PRO B 465 "    0.169 5.00e-02 4.00e+02
        pdb=" CA  PRO B 465 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 465 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  23 "   -0.064 5.00e-02 4.00e+02   9.63e-02 1.48e+01
        pdb=" N   PRO B  24 "    0.167 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "   -0.057 5.00e-02 4.00e+02
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 125
        2.52 -     3.11: 7804
        3.11 -     3.71: 14696
        3.71 -     4.30: 19355
        4.30 -     4.90: 29808
  Nonbonded interactions: 71788
  Sorted by model distance:
  nonbonded pdb=" O   HIS B 560 "
            pdb=" CG  HIS B 560 "
     model   vdw
     1.922 3.260
  nonbonded pdb=" O   THR B  22 "
            pdb=" CB  THR B  22 "
     model   vdw
     1.946 2.776
  nonbonded pdb=" O   ILE A 334 "
            pdb=" CG2 ILE A 334 "
     model   vdw
     1.964 3.460
  nonbonded pdb=" N   ASN A 163 "
            pdb=" O   ASN A 163 "
     model   vdw
     2.011 2.496
  nonbonded pdb=" O   LEU A 159 "
            pdb=" O   ASN A 163 "
     model   vdw
     2.020 3.040
  ... (remaining 71783 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: 0.02
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:             0.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.640
  Find NCS groups from input model:        0.120
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
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      :  0.006   0.136   8920  Z= 0.309
  Angle     :  1.994  38.462  12072  Z= 1.215
  Chirality :  0.121   1.414   1462
  Planarity :  0.009   0.189   1514
  Dihedral  : 13.299  80.367   3298
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 29.46
  Ramachandran Plot:
    Outliers :  0.62 %
    Allowed  : 10.28 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  1.35 %
    Favored  : 98.44 %
  Cbeta Deviations :  4.19 %
  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: -1.40 (0.24), residues: 1138
  helix:  0.15 (0.18), residues: 753
  sheet: -0.27 (0.62), residues: 74
  loop : -3.81 (0.30), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 414 
 TYR   0.022   0.002   TYR B 289 
 PHE   0.038   0.003   PHE B  74 
 TRP   0.018   0.003   TRP B 413 
 HIS   0.007   0.002   HIS A 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 8920)
  covalent geometry    : angle       1.99444 (12072)
  hydrogen bonds       : bond        0.13434 (  610)
  hydrogen bonds       : angle       6.78693 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 197
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLN cc_start: 0.9021 (tp40) cc_final: 0.8790 (mm110)
REVERT: A   91 ASN cc_start: 0.9304 (m-40) cc_final: 0.9030 (m-40)
REVERT: A  205 LEU cc_start: 0.9660 (tp) cc_final: 0.9428 (tp)
REVERT: A  427 MET cc_start: 0.8340 (mpp) cc_final: 0.7816 (mpp)
REVERT: A  454 MET cc_start: 0.8265 (mmp) cc_final: 0.8060 (mpp)
REVERT: B  208 GLN cc_start: 0.9372 (tm-30) cc_final: 0.9053 (tm-30)
REVERT: B  225 GLU cc_start: 0.8799 (tp30) cc_final: 0.8191 (tp30)
REVERT: B  292 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8657 (tm-30)
REVERT: B  410 LEU cc_start: 0.9481 (tp) cc_final: 0.9250 (tp)
REVERT: B  413 TRP cc_start: 0.8416 (t60) cc_final: 0.8032 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 199
  average time/residue: 0.0768
  time to fit residues: 22.2517
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:   20.0000
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.0050
   overall best weight:    2.9600

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
A 272 GLN
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 HIS
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 519 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.122313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.082517 restraints weight = 25855.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.085191 restraints weight = 16598.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.087040 restraints weight = 12067.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.088350 restraints weight = 9550.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.089336 restraints weight = 8032.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   8920  Z= 0.234
  Angle     :  0.846  13.472  12072  Z= 0.447
  Chirality :  0.047   0.308   1462
  Planarity :  0.007   0.077   1514
  Dihedral  :  6.021  30.351   1222
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.98
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  8.61 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  7.28 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.00 (0.24), residues: 1138
  helix:  0.49 (0.18), residues: 752
  sheet:  0.36 (0.67), residues: 63
  loop : -3.71 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 484 
 TYR   0.017   0.002   TYR A 408 
 PHE   0.027   0.003   PHE B 460 
 TRP   0.015   0.002   TRP B 413 
 HIS   0.007   0.002   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 8920)
  covalent geometry    : angle       0.84587 (12072)
  hydrogen bonds       : bond        0.06021 (  610)
  hydrogen bonds       : angle       5.85033 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9497 (ttmt) cc_final: 0.9134 (tptm)
REVERT: A   91 ASN cc_start: 0.9310 (m-40) cc_final: 0.9089 (m-40)
REVERT: A  101 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8409 (tt0)
REVERT: A  131 THR cc_start: 0.9383 (p) cc_final: 0.9082 (p)
REVERT: A  231 MET cc_start: 0.8919 (mpp) cc_final: 0.8698 (mpp)
REVERT: A  317 MET cc_start: 0.8935 (mmt) cc_final: 0.8563 (mmm)
REVERT: A  414 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8769 (ttm-80)
REVERT: A  427 MET cc_start: 0.8202 (mpp) cc_final: 0.7678 (mpp)
REVERT: B  208 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9116 (tm-30)
REVERT: B  225 GLU cc_start: 0.8847 (tp30) cc_final: 0.8141 (tp30)
REVERT: B  410 LEU cc_start: 0.9436 (tp) cc_final: 0.9232 (tp)
REVERT: B  413 TRP cc_start: 0.8331 (t60) cc_final: 0.7985 (t60)
REVERT: B  500 LEU cc_start: 0.9243 (tp) cc_final: 0.9035 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 202
  average time/residue: 0.0779
  time to fit residues: 23.1363
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 147
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 59 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 102 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 519 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.125282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.085413 restraints weight = 25212.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088275 restraints weight = 16112.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.090337 restraints weight = 11650.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.091847 restraints weight = 9118.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.092778 restraints weight = 7581.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8920  Z= 0.165
  Angle     :  0.770  11.933  12072  Z= 0.401
  Chirality :  0.046   0.263   1462
  Planarity :  0.006   0.073   1514
  Dihedral  :  5.817  34.747   1222
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 17.58
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.00 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  5.72 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.71 (0.25), residues: 1138
  helix:  0.77 (0.18), residues: 755
  sheet:  0.31 (0.67), residues: 63
  loop : -3.78 (0.28), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 345 
 TYR   0.017   0.002   TYR B 408 
 PHE   0.021   0.002   PHE B 304 
 TRP   0.011   0.001   TRP B 413 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 8920)
  covalent geometry    : angle       0.77027 (12072)
  hydrogen bonds       : bond        0.05471 (  610)
  hydrogen bonds       : angle       5.51144 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 201
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9243 (tttt) cc_final: 0.8809 (ttmt)
REVERT: A   91 ASN cc_start: 0.9255 (m-40) cc_final: 0.9019 (m-40)
REVERT: A  101 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8583 (tt0)
REVERT: A  153 ILE cc_start: 0.8751 (mm) cc_final: 0.8517 (tp)
REVERT: A  427 MET cc_start: 0.8175 (mpp) cc_final: 0.7585 (mpp)
REVERT: A  567 HIS cc_start: 0.6982 (t-90) cc_final: 0.6578 (p90)
REVERT: B  208 GLN cc_start: 0.9472 (tm-30) cc_final: 0.9064 (tm-30)
REVERT: B  217 LYS cc_start: 0.9265 (tptt) cc_final: 0.8946 (tptt)
REVERT: B  225 GLU cc_start: 0.8822 (tp30) cc_final: 0.8095 (tp30)
REVERT: B  292 GLN cc_start: 0.8977 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: B  413 TRP cc_start: 0.8296 (t60) cc_final: 0.7988 (t60)
REVERT: B  454 MET cc_start: 0.8646 (mmp) cc_final: 0.8430 (mmm)
  outliers start: 2
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0782
  time to fit residues: 23.1127
Evaluate side-chains
  152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 35 optimal weight:    7.9990
   chunk 70 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0270
   chunk 75 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 272 GLN
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.127219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.086162 restraints weight = 25366.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.089102 restraints weight = 16159.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.091153 restraints weight = 11683.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.092691 restraints weight = 9190.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.093561 restraints weight = 7683.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8920  Z= 0.160
  Angle     :  0.764  11.864  12072  Z= 0.394
  Chirality :  0.046   0.233   1462
  Planarity :  0.006   0.074   1514
  Dihedral  :  5.674  33.794   1222
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.08 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.89 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.55 (0.25), residues: 1138
  helix:  0.90 (0.18), residues: 756
  sheet:  0.03 (0.66), residues: 63
  loop : -3.67 (0.29), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 345 
 TYR   0.019   0.001   TYR A 408 
 PHE   0.051   0.003   PHE A 384 
 TRP   0.006   0.001   TRP B 413 
 HIS   0.005   0.001   HIS A 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 8920)
  covalent geometry    : angle       0.76366 (12072)
  hydrogen bonds       : bond        0.05226 (  610)
  hydrogen bonds       : angle       5.34756 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 204
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9168 (tttt) cc_final: 0.8791 (tppt)
REVERT: A   91 ASN cc_start: 0.9203 (m-40) cc_final: 0.8987 (m-40)
REVERT: A  101 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8530 (tt0)
REVERT: A  106 LYS cc_start: 0.9517 (tptm) cc_final: 0.9292 (tptm)
REVERT: A  131 THR cc_start: 0.9310 (p) cc_final: 0.9066 (p)
REVERT: A  153 ILE cc_start: 0.8678 (mm) cc_final: 0.8456 (tp)
REVERT: A  231 MET cc_start: 0.8907 (mpp) cc_final: 0.8652 (mpp)
REVERT: A  317 MET cc_start: 0.8930 (mmt) cc_final: 0.8517 (mmm)
REVERT: A  327 ASP cc_start: 0.9030 (t0) cc_final: 0.8713 (t0)
REVERT: A  427 MET cc_start: 0.8141 (mpp) cc_final: 0.7583 (mpp)
REVERT: A  501 MET cc_start: 0.9216 (tmm) cc_final: 0.8929 (tmm)
REVERT: A  567 HIS cc_start: 0.7012 (t-90) cc_final: 0.6603 (p90)
REVERT: B  217 LYS cc_start: 0.9319 (tptt) cc_final: 0.8969 (tptt)
REVERT: B  225 GLU cc_start: 0.8763 (tp30) cc_final: 0.8030 (tp30)
REVERT: B  292 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8354 (tm-30)
REVERT: B  454 MET cc_start: 0.8663 (mmp) cc_final: 0.8447 (mmm)
  outliers start: 3
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0750
  time to fit residues: 22.7623
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 112 optimal weight:   30.0000
   chunk 2 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 4 optimal weight:    0.7980
   chunk 109 optimal weight:    8.9990
   chunk 105 optimal weight:   10.0000
   chunk 62 optimal weight:    0.0270
   chunk 63 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 90 optimal weight:   20.0000
   overall best weight:    0.7442

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.127475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.087069 restraints weight = 25688.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.090015 restraints weight = 16259.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.092207 restraints weight = 11712.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.093732 restraints weight = 9113.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.094735 restraints weight = 7578.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8920  Z= 0.169
  Angle     :  0.762  12.090  12072  Z= 0.392
  Chirality :  0.046   0.231   1462
  Planarity :  0.006   0.072   1514
  Dihedral  :  5.602  34.125   1222
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.73 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  4.16 %
    Favored  : 95.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.49 (0.25), residues: 1138
  helix:  0.98 (0.19), residues: 755
  sheet:  0.00 (0.67), residues: 63
  loop : -3.72 (0.29), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 345 
 TYR   0.024   0.002   TYR B 408 
 PHE   0.037   0.002   PHE B  74 
 TRP   0.017   0.001   TRP B 413 
 HIS   0.003   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8920)
  covalent geometry    : angle       0.76165 (12072)
  hydrogen bonds       : bond        0.05075 (  610)
  hydrogen bonds       : angle       5.25277 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9147 (tttt) cc_final: 0.8775 (ttmm)
REVERT: A   91 ASN cc_start: 0.9214 (m-40) cc_final: 0.8951 (t0)
REVERT: A  101 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8365 (tt0)
REVERT: A  225 GLU cc_start: 0.8665 (tp30) cc_final: 0.7605 (tp30)
REVERT: A  231 MET cc_start: 0.8927 (mpp) cc_final: 0.8674 (mpp)
REVERT: A  384 PHE cc_start: 0.8453 (m-10) cc_final: 0.8191 (m-80)
REVERT: A  414 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8582 (ttp-110)
REVERT: A  427 MET cc_start: 0.8157 (mpp) cc_final: 0.7577 (mpp)
REVERT: A  567 HIS cc_start: 0.7045 (t-90) cc_final: 0.6605 (p90)
REVERT: B  217 LYS cc_start: 0.9338 (tptt) cc_final: 0.8596 (tptt)
REVERT: B  225 GLU cc_start: 0.8780 (tp30) cc_final: 0.8016 (tp30)
REVERT: B  410 LEU cc_start: 0.9437 (tp) cc_final: 0.9235 (tp)
REVERT: B  413 TRP cc_start: 0.8421 (t60) cc_final: 0.8099 (t60)
REVERT: B  454 MET cc_start: 0.8525 (mmp) cc_final: 0.8313 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 202
  average time/residue: 0.0755
  time to fit residues: 22.3057
Evaluate side-chains
  150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 104 optimal weight:    0.2980
   chunk 54 optimal weight:    8.9990
   chunk 90 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 32 optimal weight:   30.0000
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 HIS
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 GLN
B 561 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.126249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087338 restraints weight = 25151.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090352 restraints weight = 15775.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.092471 restraints weight = 11266.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.094047 restraints weight = 8747.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.095065 restraints weight = 7212.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8920  Z= 0.160
  Angle     :  0.765  12.242  12072  Z= 0.394
  Chirality :  0.046   0.223   1462
  Planarity :  0.006   0.069   1514
  Dihedral  :  5.565  35.232   1222
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.73 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.81 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.43 (0.25), residues: 1138
  helix:  1.03 (0.19), residues: 755
  sheet: -0.03 (0.66), residues: 63
  loop : -3.67 (0.30), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 345 
 TYR   0.019   0.002   TYR B 408 
 PHE   0.043   0.002   PHE A 160 
 TRP   0.011   0.001   TRP B 413 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 8920)
  covalent geometry    : angle       0.76495 (12072)
  hydrogen bonds       : bond        0.04973 (  610)
  hydrogen bonds       : angle       5.16754 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9123 (tttt) cc_final: 0.8724 (ttmm)
REVERT: A   91 ASN cc_start: 0.9155 (m-40) cc_final: 0.8915 (m-40)
REVERT: A  101 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8215 (tt0)
REVERT: A  131 THR cc_start: 0.9236 (p) cc_final: 0.8977 (p)
REVERT: A  197 ASP cc_start: 0.8924 (t70) cc_final: 0.8451 (m-30)
REVERT: A  225 GLU cc_start: 0.8756 (tp30) cc_final: 0.7632 (tp30)
REVERT: A  231 MET cc_start: 0.8967 (mpp) cc_final: 0.8723 (mpp)
REVERT: A  317 MET cc_start: 0.8922 (mmt) cc_final: 0.8497 (mmm)
REVERT: A  384 PHE cc_start: 0.8592 (m-10) cc_final: 0.8305 (m-80)
REVERT: A  427 MET cc_start: 0.8243 (mpp) cc_final: 0.7554 (mpp)
REVERT: A  456 TYR cc_start: 0.6741 (t80) cc_final: 0.6461 (t80)
REVERT: A  567 HIS cc_start: 0.7003 (t-90) cc_final: 0.6553 (p90)
REVERT: B  410 LEU cc_start: 0.9461 (tp) cc_final: 0.9224 (tp)
REVERT: B  413 TRP cc_start: 0.8490 (t60) cc_final: 0.8143 (t60)
REVERT: B  454 MET cc_start: 0.8492 (mmp) cc_final: 0.8275 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0752
  time to fit residues: 21.7238
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 46 optimal weight:   20.0000
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 45 optimal weight:    0.0060
   chunk 48 optimal weight:   30.0000
   chunk 70 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.9198

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 483 GLN
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.127031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.087583 restraints weight = 25490.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.090601 restraints weight = 16203.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.092809 restraints weight = 11594.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.094285 restraints weight = 9001.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.095444 restraints weight = 7474.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8920  Z= 0.153
  Angle     :  0.773  12.639  12072  Z= 0.395
  Chirality :  0.046   0.216   1462
  Planarity :  0.006   0.069   1514
  Dihedral  :  5.525  34.908   1222
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 16.63
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  8.26 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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 (0.25), residues: 1138
  helix:  1.04 (0.19), residues: 752
  sheet: -0.06 (0.66), residues: 63
  loop : -3.67 (0.29), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 345 
 TYR   0.023   0.002   TYR A 268 
 PHE   0.033   0.002   PHE B  74 
 TRP   0.009   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8920)
  covalent geometry    : angle       0.77273 (12072)
  hydrogen bonds       : bond        0.04846 (  610)
  hydrogen bonds       : angle       5.12149 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9236 (tttt) cc_final: 0.8896 (tptt)
REVERT: A  197 ASP cc_start: 0.8915 (t70) cc_final: 0.8443 (m-30)
REVERT: A  225 GLU cc_start: 0.8747 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  231 MET cc_start: 0.8924 (mpp) cc_final: 0.8712 (mpp)
REVERT: A  384 PHE cc_start: 0.8767 (m-10) cc_final: 0.8457 (m-80)
REVERT: A  427 MET cc_start: 0.8127 (mpp) cc_final: 0.7383 (mpp)
REVERT: A  456 TYR cc_start: 0.6701 (t80) cc_final: 0.6473 (t80)
REVERT: A  501 MET cc_start: 0.9220 (tmm) cc_final: 0.9018 (tmm)
REVERT: A  567 HIS cc_start: 0.7005 (t-90) cc_final: 0.6532 (p-80)
REVERT: B  217 LYS cc_start: 0.9438 (tptt) cc_final: 0.8929 (tptt)
REVERT: B  225 GLU cc_start: 0.8655 (tp30) cc_final: 0.8048 (tp30)
REVERT: B  292 GLN cc_start: 0.8919 (tm-30) cc_final: 0.8322 (tm-30)
REVERT: B  410 LEU cc_start: 0.9450 (tp) cc_final: 0.9191 (tp)
REVERT: B  413 TRP cc_start: 0.8360 (t60) cc_final: 0.8057 (t60)
REVERT: B  454 MET cc_start: 0.8482 (mmp) cc_final: 0.8269 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0810
  time to fit residues: 22.0924
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 94 optimal weight:    5.9990
   chunk 80 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 41 optimal weight:    0.0870
   chunk 113 optimal weight:   10.0000
   chunk 8 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.128555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.089801 restraints weight = 24964.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.092842 restraints weight = 15789.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.094999 restraints weight = 11260.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.096463 restraints weight = 8741.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.097663 restraints weight = 7247.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8920  Z= 0.151
  Angle     :  0.771  12.876  12072  Z= 0.392
  Chirality :  0.046   0.218   1462
  Planarity :  0.006   0.081   1514
  Dihedral  :  5.480  34.269   1222
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.64 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.37 (0.25), residues: 1138
  helix:  1.09 (0.19), residues: 754
  sheet: -0.46 (0.63), residues: 68
  loop : -3.62 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG B 345 
 TYR   0.014   0.001   TYR A 268 
 PHE   0.032   0.002   PHE B  74 
 TRP   0.007   0.001   TRP A 413 
 HIS   0.004   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8920)
  covalent geometry    : angle       0.77131 (12072)
  hydrogen bonds       : bond        0.04782 (  610)
  hydrogen bonds       : angle       5.07903 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9205 (tttt) cc_final: 0.8881 (tptt)
REVERT: A   59 MET cc_start: 0.7218 (mpp) cc_final: 0.6998 (mpp)
REVERT: A  197 ASP cc_start: 0.8915 (t70) cc_final: 0.8450 (m-30)
REVERT: A  225 GLU cc_start: 0.8800 (tp30) cc_final: 0.7687 (tp30)
REVERT: A  317 MET cc_start: 0.8911 (mmt) cc_final: 0.8506 (mmm)
REVERT: A  384 PHE cc_start: 0.8755 (m-10) cc_final: 0.8436 (m-80)
REVERT: A  427 MET cc_start: 0.8142 (mpp) cc_final: 0.7621 (mpp)
REVERT: A  456 TYR cc_start: 0.6682 (t80) cc_final: 0.6470 (t80)
REVERT: A  461 ILE cc_start: 0.6491 (mt) cc_final: 0.6196 (mt)
REVERT: A  501 MET cc_start: 0.9237 (tmm) cc_final: 0.9034 (tmm)
REVERT: A  567 HIS cc_start: 0.7066 (t-90) cc_final: 0.6522 (p90)
REVERT: B  217 LYS cc_start: 0.9379 (tptt) cc_final: 0.8854 (tptt)
REVERT: B  225 GLU cc_start: 0.8663 (tp30) cc_final: 0.8000 (tp30)
REVERT: B  292 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: B  410 LEU cc_start: 0.9453 (tp) cc_final: 0.9200 (tp)
REVERT: B  454 MET cc_start: 0.8488 (mmp) cc_final: 0.8278 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.0768
  time to fit residues: 21.3068
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 50 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.128141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.087898 restraints weight = 26035.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.090833 restraints weight = 16603.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.092879 restraints weight = 12022.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.094265 restraints weight = 9458.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095449 restraints weight = 7963.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8920  Z= 0.163
  Angle     :  0.786  13.087  12072  Z= 0.400
  Chirality :  0.046   0.229   1462
  Planarity :  0.006   0.066   1514
  Dihedral  :  5.496  35.706   1222
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.91 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -0.39 (0.25), residues: 1138
  helix:  1.04 (0.19), residues: 754
  sheet: -0.32 (0.65), residues: 68
  loop : -3.57 (0.30), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 345 
 TYR   0.029   0.002   TYR B 408 
 PHE   0.032   0.002   PHE B  74 
 TRP   0.019   0.002   TRP B 413 
 HIS   0.003   0.001   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8920)
  covalent geometry    : angle       0.78625 (12072)
  hydrogen bonds       : bond        0.04837 (  610)
  hydrogen bonds       : angle       5.12598 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9258 (tttt) cc_final: 0.8933 (tptt)
REVERT: A  101 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8502 (mt-10)
REVERT: A  197 ASP cc_start: 0.8915 (t70) cc_final: 0.8469 (m-30)
REVERT: A  317 MET cc_start: 0.8817 (mmt) cc_final: 0.8481 (mmm)
REVERT: A  365 GLU cc_start: 0.9011 (tp30) cc_final: 0.8749 (tp30)
REVERT: A  384 PHE cc_start: 0.8844 (m-10) cc_final: 0.8538 (m-80)
REVERT: A  414 ARG cc_start: 0.8874 (ptp-110) cc_final: 0.8256 (ptp90)
REVERT: A  427 MET cc_start: 0.8259 (mpp) cc_final: 0.7396 (mpp)
REVERT: A  456 TYR cc_start: 0.6722 (t80) cc_final: 0.6485 (t80)
REVERT: A  567 HIS cc_start: 0.6919 (t-90) cc_final: 0.6401 (p90)
REVERT: B  152 VAL cc_start: 0.9232 (t) cc_final: 0.8968 (m)
REVERT: B  212 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8741 (mp0)
REVERT: B  225 GLU cc_start: 0.8667 (tp30) cc_final: 0.7992 (tp30)
REVERT: B  289 TYR cc_start: 0.6943 (t80) cc_final: 0.6610 (t80)
REVERT: B  292 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8226 (tm-30)
REVERT: B  410 LEU cc_start: 0.9466 (tp) cc_final: 0.9198 (tp)
REVERT: B  413 TRP cc_start: 0.8397 (t60) cc_final: 0.8051 (t60)
REVERT: B  454 MET cc_start: 0.8475 (mmp) cc_final: 0.8246 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0838
  time to fit residues: 22.6026
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0670
   chunk 39 optimal weight:    0.0670
   overall best weight:    1.4262

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.127816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.087564 restraints weight = 26054.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.090489 restraints weight = 16686.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.092582 restraints weight = 12025.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.094104 restraints weight = 9440.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.094978 restraints weight = 7874.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8920  Z= 0.166
  Angle     :  0.801  13.166  12072  Z= 0.407
  Chirality :  0.046   0.209   1462
  Planarity :  0.006   0.075   1514
  Dihedral  :  5.466  36.184   1222
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.64 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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 (0.25), residues: 1138
  helix:  1.01 (0.19), residues: 755
  sheet: -0.69 (0.64), residues: 73
  loop : -3.56 (0.31), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 345 
 TYR   0.025   0.002   TYR B 408 
 PHE   0.021   0.002   PHE B  57 
 TRP   0.015   0.001   TRP B 413 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8920)
  covalent geometry    : angle       0.80086 (12072)
  hydrogen bonds       : bond        0.04856 (  610)
  hydrogen bonds       : angle       5.18154 ( 1812)

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

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

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2276 Ramachandran restraints generated.
    1138 Oldfield, 0 Emsley, 1138 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LYS cc_start: 0.9103 (tttt) cc_final: 0.8722 (tptt)
REVERT: A   59 MET cc_start: 0.7300 (mpp) cc_final: 0.7075 (mpp)
REVERT: A  101 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8579 (mt-10)
REVERT: A  197 ASP cc_start: 0.8915 (t70) cc_final: 0.8449 (m-30)
REVERT: A  205 LEU cc_start: 0.9497 (tp) cc_final: 0.9271 (tp)
REVERT: A  317 MET cc_start: 0.8771 (mmt) cc_final: 0.8467 (mmm)
REVERT: A  365 GLU cc_start: 0.8958 (tp30) cc_final: 0.8757 (tp30)
REVERT: A  384 PHE cc_start: 0.8855 (m-10) cc_final: 0.8544 (m-80)
REVERT: A  427 MET cc_start: 0.8234 (mpp) cc_final: 0.7715 (mpp)
REVERT: A  456 TYR cc_start: 0.6757 (t80) cc_final: 0.6477 (t80)
REVERT: B   57 PHE cc_start: 0.7898 (p90) cc_final: 0.7623 (p90)
REVERT: B  152 VAL cc_start: 0.9251 (t) cc_final: 0.9006 (m)
REVERT: B  225 GLU cc_start: 0.8709 (tp30) cc_final: 0.8020 (tp30)
REVERT: B  292 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8223 (tm-30)
REVERT: B  410 LEU cc_start: 0.9486 (tp) cc_final: 0.9206 (tp)
REVERT: B  413 TRP cc_start: 0.8399 (t60) cc_final: 0.8035 (t60)
REVERT: B  454 MET cc_start: 0.8431 (mmp) cc_final: 0.8188 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 185
  average time/residue: 0.0853
  time to fit residues: 22.9825
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 107 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    0.1980
   chunk 74 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 100 optimal weight:    0.0870
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 467 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.129846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.089367 restraints weight = 25652.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.092340 restraints weight = 16510.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.094458 restraints weight = 11979.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.095859 restraints weight = 9422.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.097088 restraints weight = 7924.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8920  Z= 0.153
  Angle     :  0.792  12.994  12072  Z= 0.398
  Chirality :  0.045   0.210   1462
  Planarity :  0.006   0.069   1514
  Dihedral  :  5.393  34.463   1222
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  7.38 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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 (0.25), residues: 1138
  helix:  1.11 (0.19), residues: 754
  sheet: -0.13 (0.66), residues: 68
  loop : -3.48 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG B 345 
 TYR   0.026   0.001   TYR B 408 
 PHE   0.017   0.001   PHE B  57 
 TRP   0.019   0.002   TRP A 413 
 HIS   0.003   0.001   HIS A 567 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8920)
  covalent geometry    : angle       0.79214 (12072)
  hydrogen bonds       : bond        0.04668 (  610)
  hydrogen bonds       : angle       5.08234 ( 1812)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1509.77 seconds
wall clock time: 26 minutes 55.76 seconds (1615.76 seconds total)