Starting phenix.real_space_refine
on Sun Apr  5 12:13:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/21al_67470/04_2026/21al_67470.cif"
  }
  resolution = 3.57
  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=   0.006 sd=   0.088
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      52      5.16       5
     C    6620      2.51       5
     N    1760      2.21       5
     O    1932      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10364
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2591
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 315}
          Chain breaks: 2
  Restraints were copied for chains:
    B, C, D
  Time building chain proxies: 2.06, per 1000 atoms: 0.20
  Number of scatterers: 10364
  At special positions: 0
  Unit cell: (90.28, 90.28, 97.68, 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      52     16.00
     O    1932      8.00
     N    1760      7.00
     C    6620      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: 0.83
  Conformation dependent library (CDL) restraints added in 451.4 milliseconds
  

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2488

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 4 sheets defined
      65.6% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 62 through 68
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 85 through 94
    Processing helix  chain 'A' and resid 129 through 150
    Processing helix  chain 'A' and resid 152 through 158
    Processing helix  chain 'A' and resid 159 through 173
      removed outlier: 4.000A  pdb=" N   LYS A 163 " --> pdb=" O   ALA A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 182
      removed outlier: 3.737A  pdb=" N   GLY A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 200
      removed outlier: 3.820A  pdb=" N   GLN A 200 " --> pdb=" O   TRP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 213
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 235 through 245
    Processing helix  chain 'A' and resid 250 through 254
      removed outlier: 3.955A  pdb=" N   LEU A 253 " --> pdb=" O   ASP A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 276
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 288 through 298
      removed outlier: 3.510A  pdb=" N   ALA A 291 " --> pdb=" O   HIS A 288 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE A 292 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 332 through 340
    Processing helix  chain 'A' and resid 354 through 365
      removed outlier: 3.528A  pdb=" N   ILE A 364 " --> pdb=" O   ILE A 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 61
    Processing helix  chain 'B' and resid 62 through 68
    Processing helix  chain 'B' and resid 72 through 83
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 129 through 150
    Processing helix  chain 'B' and resid 152 through 158
    Processing helix  chain 'B' and resid 159 through 173
      removed outlier: 4.000A  pdb=" N   LYS B 163 " --> pdb=" O   ALA B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 182
      removed outlier: 3.737A  pdb=" N   GLY B 179 " --> pdb=" O   ARG B 175 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU B 180 " --> pdb=" O   PRO B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 200
      removed outlier: 3.820A  pdb=" N   GLN B 200 " --> pdb=" O   TRP B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 213
    Processing helix  chain 'B' and resid 218 through 231
    Processing helix  chain 'B' and resid 235 through 245
    Processing helix  chain 'B' and resid 250 through 254
      removed outlier: 3.955A  pdb=" N   LEU B 253 " --> pdb=" O   ASP B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 276
    Processing helix  chain 'B' and resid 279 through 283
    Processing helix  chain 'B' and resid 288 through 298
      removed outlier: 3.510A  pdb=" N   ALA B 291 " --> pdb=" O   HIS B 288 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE B 292 " --> pdb=" O   PRO B 289 " (cutoff:3.500A)
      Proline residue:  B 296  - end of helix
    Processing helix  chain 'B' and resid 299 through 314
    Processing helix  chain 'B' and resid 332 through 340
    Processing helix  chain 'B' and resid 354 through 365
      removed outlier: 3.528A  pdb=" N   ILE B 364 " --> pdb=" O   ILE B 360 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 61
    Processing helix  chain 'C' and resid 62 through 68
    Processing helix  chain 'C' and resid 72 through 83
    Processing helix  chain 'C' and resid 85 through 94
    Processing helix  chain 'C' and resid 129 through 150
    Processing helix  chain 'C' and resid 152 through 158
    Processing helix  chain 'C' and resid 159 through 173
      removed outlier: 4.000A  pdb=" N   LYS C 163 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 175 through 182
      removed outlier: 3.737A  pdb=" N   GLY C 179 " --> pdb=" O   ARG C 175 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU C 180 " --> pdb=" O   PRO C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 190 through 200
      removed outlier: 3.820A  pdb=" N   GLN C 200 " --> pdb=" O   TRP C 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 213
    Processing helix  chain 'C' and resid 218 through 231
    Processing helix  chain 'C' and resid 235 through 245
    Processing helix  chain 'C' and resid 250 through 254
      removed outlier: 3.955A  pdb=" N   LEU C 253 " --> pdb=" O   ASP C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 255 through 276
    Processing helix  chain 'C' and resid 279 through 283
    Processing helix  chain 'C' and resid 288 through 298
      removed outlier: 3.510A  pdb=" N   ALA C 291 " --> pdb=" O   HIS C 288 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE C 292 " --> pdb=" O   PRO C 289 " (cutoff:3.500A)
      Proline residue:  C 296  - end of helix
    Processing helix  chain 'C' and resid 299 through 314
    Processing helix  chain 'C' and resid 332 through 340
    Processing helix  chain 'C' and resid 354 through 365
      removed outlier: 3.528A  pdb=" N   ILE C 364 " --> pdb=" O   ILE C 360 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 61
    Processing helix  chain 'D' and resid 62 through 68
    Processing helix  chain 'D' and resid 72 through 83
    Processing helix  chain 'D' and resid 85 through 94
    Processing helix  chain 'D' and resid 129 through 150
    Processing helix  chain 'D' and resid 152 through 158
    Processing helix  chain 'D' and resid 159 through 173
      removed outlier: 4.000A  pdb=" N   LYS D 163 " --> pdb=" O   ALA D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 175 through 182
      removed outlier: 3.737A  pdb=" N   GLY D 179 " --> pdb=" O   ARG D 175 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU D 180 " --> pdb=" O   PRO D 176 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 190 through 200
      removed outlier: 3.820A  pdb=" N   GLN D 200 " --> pdb=" O   TRP D 196 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 202 through 213
    Processing helix  chain 'D' and resid 218 through 231
    Processing helix  chain 'D' and resid 235 through 245
    Processing helix  chain 'D' and resid 250 through 254
      removed outlier: 3.955A  pdb=" N   LEU D 253 " --> pdb=" O   ASP D 250 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 276
    Processing helix  chain 'D' and resid 279 through 283
    Processing helix  chain 'D' and resid 288 through 298
      removed outlier: 3.510A  pdb=" N   ALA D 291 " --> pdb=" O   HIS D 288 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE D 292 " --> pdb=" O   PRO D 289 " (cutoff:3.500A)
      Proline residue:  D 296  - end of helix
    Processing helix  chain 'D' and resid 299 through 314
    Processing helix  chain 'D' and resid 332 through 340
    Processing helix  chain 'D' and resid 354 through 365
      removed outlier: 3.528A  pdb=" N   ILE D 364 " --> pdb=" O   ILE D 360 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 99 through 100
    Processing sheet with id=2, first strand: chain 'B' and resid 99 through 100
    Processing sheet with id=3, first strand: chain 'C' and resid 99 through 100
    Processing sheet with id=4, first strand: chain 'D' and resid 99 through 100

    548 hydrogen bonds defined for protein.
    1560 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: 1.60

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1816
        1.32 -     1.44: 2652
        1.44 -     1.57: 6036
        1.57 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 10592
  Sorted by residual:
  bond pdb=" CG  HIS D 288 "
       pdb=" CD2 HIS D 288 "
    ideal  model  delta    sigma   weight residual
    1.354  1.318  0.036 1.10e-02 8.26e+03 1.09e+01
  bond pdb=" CG  HIS B 288 "
       pdb=" CD2 HIS B 288 "
    ideal  model  delta    sigma   weight residual
    1.354  1.318  0.036 1.10e-02 8.26e+03 1.09e+01
  bond pdb=" CG  HIS A 288 "
       pdb=" CD2 HIS A 288 "
    ideal  model  delta    sigma   weight residual
    1.354  1.318  0.036 1.10e-02 8.26e+03 1.09e+01
  bond pdb=" CG  HIS C 288 "
       pdb=" CD2 HIS C 288 "
    ideal  model  delta    sigma   weight residual
    1.354  1.318  0.036 1.10e-02 8.26e+03 1.09e+01
  bond pdb=" C   ALA A 285 "
       pdb=" O   ALA A 285 "
    ideal  model  delta    sigma   weight residual
    1.237  1.198  0.039 1.17e-02 7.31e+03 1.08e+01
  ... (remaining 10587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 10712
        1.91 -     3.81: 3000
        3.81 -     5.72: 540
        5.72 -     7.62: 76
        7.62 -     9.53: 12
  Bond angle restraints: 14340
  Sorted by residual:
  angle pdb=" CA  ASP C 250 "
        pdb=" CB  ASP C 250 "
        pdb=" CG  ASP C 250 "
      ideal   model   delta    sigma   weight residual
     112.60  119.85   -7.25 1.00e+00 1.00e+00 5.26e+01
  angle pdb=" CA  ASP B 250 "
        pdb=" CB  ASP B 250 "
        pdb=" CG  ASP B 250 "
      ideal   model   delta    sigma   weight residual
     112.60  119.85   -7.25 1.00e+00 1.00e+00 5.26e+01
  angle pdb=" CA  ASP D 250 "
        pdb=" CB  ASP D 250 "
        pdb=" CG  ASP D 250 "
      ideal   model   delta    sigma   weight residual
     112.60  119.85   -7.25 1.00e+00 1.00e+00 5.26e+01
  angle pdb=" CA  ASP A 250 "
        pdb=" CB  ASP A 250 "
        pdb=" CG  ASP A 250 "
      ideal   model   delta    sigma   weight residual
     112.60  119.85   -7.25 1.00e+00 1.00e+00 5.26e+01
  angle pdb=" CA  THR D 254 "
        pdb=" CB  THR D 254 "
        pdb=" OG1 THR D 254 "
      ideal   model   delta    sigma   weight residual
     109.60  101.09    8.51 1.50e+00 4.44e-01 3.22e+01
  ... (remaining 14335 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.54: 5624
       13.54 -    27.08: 608
       27.08 -    40.63: 104
       40.63 -    54.17: 40
       54.17 -    67.71: 20
  Dihedral angle restraints: 6396
    sinusoidal: 2548
      harmonic: 3848
  Sorted by residual:
  dihedral pdb=" CA  GLY C 368 "
           pdb=" C   GLY C 368 "
           pdb=" N   LEU C 369 "
           pdb=" CA  LEU C 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.49   33.51     0      5.00e+00 4.00e-02 4.49e+01
  dihedral pdb=" CA  GLY B 368 "
           pdb=" C   GLY B 368 "
           pdb=" N   LEU B 369 "
           pdb=" CA  LEU B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.49   33.51     0      5.00e+00 4.00e-02 4.49e+01
  dihedral pdb=" CA  GLY D 368 "
           pdb=" C   GLY D 368 "
           pdb=" N   LEU D 369 "
           pdb=" CA  LEU D 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.49   33.51     0      5.00e+00 4.00e-02 4.49e+01
  ... (remaining 6393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 880
       0.072 -    0.144: 520
       0.144 -    0.216: 176
       0.216 -    0.288: 52
       0.288 -    0.360: 8
  Chirality restraints: 1636
  Sorted by residual:
  chirality pdb=" CA  ARG C 346 "
            pdb=" N   ARG C 346 "
            pdb=" C   ARG C 346 "
            pdb=" CB  ARG C 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CA  ARG B 346 "
            pdb=" N   ARG B 346 "
            pdb=" C   ARG B 346 "
            pdb=" CB  ARG B 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.23e+00
  chirality pdb=" CA  ARG D 346 "
            pdb=" N   ARG D 346 "
            pdb=" C   ARG D 346 "
            pdb=" CB  ARG D 346 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.23e+00
  ... (remaining 1633 not shown)

  Planarity restraints: 1824
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 309 "   -0.061 2.00e-02 2.50e+03   3.16e-02 2.49e+01
        pdb=" CG  TRP B 309 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 309 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 309 "    0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 309 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 309 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 309 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 309 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 309 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 309 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 309 "    0.061 2.00e-02 2.50e+03   3.16e-02 2.49e+01
        pdb=" CG  TRP D 309 "   -0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 309 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 309 "   -0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 309 "    0.018 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 309 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 309 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 309 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 309 "    0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 309 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 309 "   -0.061 2.00e-02 2.50e+03   3.16e-02 2.49e+01
        pdb=" CG  TRP A 309 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 309 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 309 "    0.047 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 309 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 309 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 309 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 309 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 309 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 309 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1821 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1968
        2.80 -     3.32: 10892
        3.32 -     3.85: 17204
        3.85 -     4.37: 20324
        4.37 -     4.90: 33408
  Nonbonded interactions: 83796
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 251 "
            pdb=" OG1 THR B 254 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ALA C 251 "
            pdb=" OG1 THR C 254 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ALA A 251 "
            pdb=" OG1 THR A 254 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ALA D 251 "
            pdb=" OG1 THR D 254 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OE2 GLU A 247 "
            pdb=" OE1 GLU D 333 "
     model   vdw
     2.379 3.040
  ... (remaining 83791 not shown)

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

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:             0.010
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.230
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
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      :  0.011   0.058  10592  Z= 0.675
  Angle     :  1.810   9.525  14340  Z= 1.222
  Chirality :  0.101   0.360   1636
  Planarity :  0.011   0.108   1824
  Dihedral  : 12.412  67.707   3908
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.18 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  2.48 %
    Favored  : 97.16 %
  Cbeta Deviations :  0.32 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.32 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.10 (0.18), residues: 1312
  helix: -1.99 (0.14), residues: 792
  sheet:  None (None), residues: 0
  loop : -1.93 (0.23), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.004   ARG B 342 
 TYR   0.041   0.010   TYR C 238 
 PHE   0.061   0.008   PHE A 118 
 TRP   0.061   0.019   TRP A 309 
 HIS   0.013   0.003   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.01085 (10592)
  covalent geometry    : angle       1.80953 (14340)
  hydrogen bonds       : bond        0.18855 (  548)
  hydrogen bonds       : angle       7.21493 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 276
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8606 (mt) cc_final: 0.8167 (mp)
REVERT: A   52 ASP cc_start: 0.8922 (m-30) cc_final: 0.8434 (p0)
REVERT: A   65 ARG cc_start: 0.8913 (tpt170) cc_final: 0.8358 (tpp80)
REVERT: A   81 LEU cc_start: 0.8823 (tp) cc_final: 0.8295 (mt)
REVERT: A   82 LEU cc_start: 0.8083 (tp) cc_final: 0.7824 (tp)
REVERT: A   95 VAL cc_start: 0.9008 (t) cc_final: 0.8806 (m)
REVERT: A  188 PHE cc_start: 0.8760 (t80) cc_final: 0.8235 (t80)
REVERT: A  244 TYR cc_start: 0.9296 (t80) cc_final: 0.8549 (t80)
REVERT: A  249 MET cc_start: 0.8561 (mmm) cc_final: 0.7974 (mmm)
REVERT: A  276 HIS cc_start: 0.7807 (m-70) cc_final: 0.7420 (m-70)
REVERT: A  361 MET cc_start: 0.8204 (mmp) cc_final: 0.7884 (mmp)
REVERT: A  369 LEU cc_start: 0.8715 (mt) cc_final: 0.8346 (mp)
REVERT: B   29 LEU cc_start: 0.8603 (mt) cc_final: 0.8164 (mp)
REVERT: B   52 ASP cc_start: 0.8921 (m-30) cc_final: 0.8432 (p0)
REVERT: B   65 ARG cc_start: 0.8911 (tpt170) cc_final: 0.8358 (tpp80)
REVERT: B   81 LEU cc_start: 0.8824 (tp) cc_final: 0.8296 (mt)
REVERT: B   82 LEU cc_start: 0.8082 (tp) cc_final: 0.7821 (tp)
REVERT: B   95 VAL cc_start: 0.9009 (t) cc_final: 0.8807 (m)
REVERT: B  188 PHE cc_start: 0.8758 (t80) cc_final: 0.8232 (t80)
REVERT: B  244 TYR cc_start: 0.9296 (t80) cc_final: 0.8553 (t80)
REVERT: B  249 MET cc_start: 0.8561 (mmm) cc_final: 0.7976 (mmm)
REVERT: B  276 HIS cc_start: 0.7807 (m-70) cc_final: 0.7419 (m-70)
REVERT: B  361 MET cc_start: 0.8209 (mmp) cc_final: 0.7890 (mmp)
REVERT: B  369 LEU cc_start: 0.8717 (mt) cc_final: 0.8350 (mp)
REVERT: C   29 LEU cc_start: 0.8601 (mt) cc_final: 0.8161 (mp)
REVERT: C   52 ASP cc_start: 0.8914 (m-30) cc_final: 0.8429 (p0)
REVERT: C   65 ARG cc_start: 0.8913 (tpt170) cc_final: 0.8359 (tpp80)
REVERT: C   81 LEU cc_start: 0.8821 (tp) cc_final: 0.8292 (mt)
REVERT: C   82 LEU cc_start: 0.8081 (tp) cc_final: 0.7823 (tp)
REVERT: C   95 VAL cc_start: 0.9009 (t) cc_final: 0.8806 (m)
REVERT: C  188 PHE cc_start: 0.8759 (t80) cc_final: 0.8232 (t80)
REVERT: C  244 TYR cc_start: 0.9295 (t80) cc_final: 0.8549 (t80)
REVERT: C  249 MET cc_start: 0.8562 (mmm) cc_final: 0.7974 (mmm)
REVERT: C  276 HIS cc_start: 0.7808 (m-70) cc_final: 0.7421 (m-70)
REVERT: C  361 MET cc_start: 0.8206 (mmp) cc_final: 0.7888 (mmp)
REVERT: C  369 LEU cc_start: 0.8717 (mt) cc_final: 0.8350 (mp)
REVERT: D   29 LEU cc_start: 0.8603 (mt) cc_final: 0.8165 (mp)
REVERT: D   52 ASP cc_start: 0.8919 (m-30) cc_final: 0.8433 (p0)
REVERT: D   65 ARG cc_start: 0.8912 (tpt170) cc_final: 0.8358 (tpp80)
REVERT: D   81 LEU cc_start: 0.8824 (tp) cc_final: 0.8295 (mt)
REVERT: D   82 LEU cc_start: 0.8083 (tp) cc_final: 0.7822 (tp)
REVERT: D   95 VAL cc_start: 0.9010 (t) cc_final: 0.8809 (m)
REVERT: D  188 PHE cc_start: 0.8759 (t80) cc_final: 0.8231 (t80)
REVERT: D  244 TYR cc_start: 0.9293 (t80) cc_final: 0.8542 (t80)
REVERT: D  249 MET cc_start: 0.8562 (mmm) cc_final: 0.7974 (mmm)
REVERT: D  276 HIS cc_start: 0.7808 (m-70) cc_final: 0.7420 (m-70)
REVERT: D  361 MET cc_start: 0.8205 (mmp) cc_final: 0.7888 (mmp)
REVERT: D  369 LEU cc_start: 0.8716 (mt) cc_final: 0.8348 (mp)
  outliers start: 4
  outliers final: 4
  residues processed: 280
  average time/residue: 0.1358
  time to fit residues: 50.1784
Evaluate side-chains
  191 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 187
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain B residue  266 LEU
Chi-restraints excluded: chain C residue  266 LEU
Chi-restraints excluded: chain D residue  266 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A  56 ASN
A 125 GLN
A 178 HIS
A 198 ASN
B  55 GLN
B  56 ASN
B 125 GLN
B 178 HIS
B 198 ASN
C  55 GLN
C  56 ASN
C 125 GLN
C 178 HIS
C 198 ASN
D  55 GLN
D  56 ASN
D 125 GLN
D 178 HIS
D 198 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.188292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.131023 restraints weight = 14259.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.134972 restraints weight = 9122.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137666 restraints weight = 6778.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139368 restraints weight = 5618.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140270 restraints weight = 4991.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10592  Z= 0.128
  Angle     :  0.571   5.201  14340  Z= 0.303
  Chirality :  0.041   0.170   1636
  Planarity :  0.005   0.041   1824
  Dihedral  :  5.281  49.498   1432
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  6.74 %
    Favored  : 91.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.23), residues: 1312
  helix:  0.57 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -0.74 (0.28), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 165 
 TYR   0.007   0.001   TYR C 238 
 PHE   0.007   0.001   PHE B  33 
 TRP   0.012   0.002   TRP A 196 
 HIS   0.002   0.001   HIS A  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10592)
  covalent geometry    : angle       0.57113 (14340)
  hydrogen bonds       : bond        0.04118 (  548)
  hydrogen bonds       : angle       4.29231 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 241
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8172 (mt) cc_final: 0.7968 (mp)
REVERT: A   66 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7370 (mtm-85)
REVERT: A   69 PHE cc_start: 0.7213 (m-80) cc_final: 0.6832 (m-80)
REVERT: A  191 HIS cc_start: 0.7309 (p90) cc_final: 0.6502 (p90)
REVERT: A  195 ASP cc_start: 0.8303 (m-30) cc_final: 0.7996 (m-30)
REVERT: A  249 MET cc_start: 0.8559 (mmm) cc_final: 0.8184 (mmm)
REVERT: B   29 LEU cc_start: 0.8171 (mt) cc_final: 0.7964 (mp)
REVERT: B   66 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7372 (mtm-85)
REVERT: B   69 PHE cc_start: 0.7229 (m-80) cc_final: 0.6843 (m-80)
REVERT: B  191 HIS cc_start: 0.7320 (p90) cc_final: 0.6520 (p90)
REVERT: B  195 ASP cc_start: 0.8301 (m-30) cc_final: 0.7987 (m-30)
REVERT: B  249 MET cc_start: 0.8538 (mmm) cc_final: 0.8167 (mmm)
REVERT: C   29 LEU cc_start: 0.8171 (mt) cc_final: 0.7965 (mp)
REVERT: C   66 ARG cc_start: 0.8379 (mtm-85) cc_final: 0.7369 (mtm-85)
REVERT: C   69 PHE cc_start: 0.7224 (m-80) cc_final: 0.6832 (m-80)
REVERT: C  191 HIS cc_start: 0.7317 (p90) cc_final: 0.6515 (p90)
REVERT: C  195 ASP cc_start: 0.8305 (m-30) cc_final: 0.7991 (m-30)
REVERT: C  249 MET cc_start: 0.8531 (mmm) cc_final: 0.8166 (mmm)
REVERT: D   29 LEU cc_start: 0.8169 (mt) cc_final: 0.7964 (mp)
REVERT: D   66 ARG cc_start: 0.8376 (mtm-85) cc_final: 0.7365 (mtm-85)
REVERT: D   69 PHE cc_start: 0.7210 (m-80) cc_final: 0.6831 (m-80)
REVERT: D  191 HIS cc_start: 0.7309 (p90) cc_final: 0.6510 (p90)
REVERT: D  195 ASP cc_start: 0.8304 (m-30) cc_final: 0.7994 (m-30)
REVERT: D  249 MET cc_start: 0.8557 (mmm) cc_final: 0.8187 (mmm)
  outliers start: 16
  outliers final: 4
  residues processed: 253
  average time/residue: 0.1232
  time to fit residues: 42.0392
Evaluate side-chains
  184 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 180
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain B residue  149 ILE
Chi-restraints excluded: chain C residue  149 ILE
Chi-restraints excluded: chain D residue  149 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 104 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 88 optimal weight:    4.9990
   chunk 75 optimal weight:   40.0000
   chunk 14 optimal weight:   30.0000
   chunk 12 optimal weight:   50.0000
   chunk 95 optimal weight:    0.0970
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   overall best weight:    4.0186

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.182972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.125367 restraints weight = 14061.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.129177 restraints weight = 8844.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131691 restraints weight = 6567.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.133436 restraints weight = 5454.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.134316 restraints weight = 4857.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10592  Z= 0.174
  Angle     :  0.578   4.906  14340  Z= 0.306
  Chirality :  0.042   0.184   1636
  Planarity :  0.005   0.042   1824
  Dihedral  :  4.284  16.205   1424
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  :  9.66 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.23), residues: 1312
  helix:  0.74 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -0.61 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  65 
 TYR   0.012   0.002   TYR A 339 
 PHE   0.008   0.002   PHE D 188 
 TRP   0.009   0.002   TRP B 196 
 HIS   0.004   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10592)
  covalent geometry    : angle       0.57775 (14340)
  hydrogen bonds       : bond        0.04437 (  548)
  hydrogen bonds       : angle       4.15547 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 191
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 GLN cc_start: 0.7421 (mm-40) cc_final: 0.7203 (mm-40)
REVERT: A   61 LEU cc_start: 0.8357 (mm) cc_final: 0.8081 (mm)
REVERT: A   65 ARG cc_start: 0.8819 (mmm160) cc_final: 0.8189 (mmm160)
REVERT: A  188 PHE cc_start: 0.6967 (t80) cc_final: 0.6412 (t80)
REVERT: A  191 HIS cc_start: 0.7826 (p90) cc_final: 0.6934 (p90)
REVERT: A  195 ASP cc_start: 0.8374 (m-30) cc_final: 0.8027 (m-30)
REVERT: A  249 MET cc_start: 0.8700 (mmm) cc_final: 0.8273 (mmm)
REVERT: B   35 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7202 (mm-40)
REVERT: B   61 LEU cc_start: 0.8363 (mm) cc_final: 0.8085 (mm)
REVERT: B   65 ARG cc_start: 0.8830 (mmm160) cc_final: 0.8197 (mmm160)
REVERT: B  188 PHE cc_start: 0.6971 (t80) cc_final: 0.6416 (t80)
REVERT: B  191 HIS cc_start: 0.7826 (p90) cc_final: 0.6942 (p90)
REVERT: B  195 ASP cc_start: 0.8377 (m-30) cc_final: 0.8027 (m-30)
REVERT: B  249 MET cc_start: 0.8680 (mmm) cc_final: 0.8269 (mmm)
REVERT: C   35 GLN cc_start: 0.7426 (mm-40) cc_final: 0.7209 (mm-40)
REVERT: C   61 LEU cc_start: 0.8365 (mm) cc_final: 0.8084 (mm)
REVERT: C   65 ARG cc_start: 0.8832 (mmm160) cc_final: 0.8195 (mmm160)
REVERT: C  188 PHE cc_start: 0.6973 (t80) cc_final: 0.6415 (t80)
REVERT: C  191 HIS cc_start: 0.7821 (p90) cc_final: 0.6935 (p90)
REVERT: C  195 ASP cc_start: 0.8369 (m-30) cc_final: 0.8020 (m-30)
REVERT: C  249 MET cc_start: 0.8680 (mmm) cc_final: 0.8279 (mmm)
REVERT: D   61 LEU cc_start: 0.8366 (mm) cc_final: 0.8085 (mm)
REVERT: D   65 ARG cc_start: 0.8817 (mmm160) cc_final: 0.8189 (mmm160)
REVERT: D  188 PHE cc_start: 0.6963 (t80) cc_final: 0.6402 (t80)
REVERT: D  191 HIS cc_start: 0.7824 (p90) cc_final: 0.6937 (p90)
REVERT: D  195 ASP cc_start: 0.8378 (m-30) cc_final: 0.8031 (m-30)
REVERT: D  249 MET cc_start: 0.8697 (mmm) cc_final: 0.8285 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 203
  average time/residue: 0.1045
  time to fit residues: 30.0057
Evaluate side-chains
  183 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 75 optimal weight:   50.0000
   chunk 54 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 105 optimal weight:   10.0000
   chunk 130 optimal weight:   20.0000
   chunk 7 optimal weight:   30.0000
   chunk 46 optimal weight:    6.9990
   chunk 123 optimal weight:   20.0000
   chunk 71 optimal weight:    0.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
A 225 GLN
B  55 GLN
B 225 GLN
C  55 GLN
C 225 GLN
D  55 GLN
D 225 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.179849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.122837 restraints weight = 14383.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.126199 restraints weight = 9559.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.128470 restraints weight = 7338.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.129877 restraints weight = 6214.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.130762 restraints weight = 5611.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10592  Z= 0.223
  Angle     :  0.604   4.848  14340  Z= 0.320
  Chirality :  0.043   0.197   1636
  Planarity :  0.005   0.042   1824
  Dihedral  :  4.234  15.634   1424
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 12.94 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.23), residues: 1312
  helix:  0.59 (0.18), residues: 816
  sheet:  None (None), residues: 0
  loop : -0.70 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  65 
 TYR   0.021   0.002   TYR D 244 
 PHE   0.013   0.002   PHE A  69 
 TRP   0.012   0.002   TRP A 196 
 HIS   0.005   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (10592)
  covalent geometry    : angle       0.60381 (14340)
  hydrogen bonds       : bond        0.04510 (  548)
  hydrogen bonds       : angle       4.25031 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 160
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7955 (mt)
REVERT: A  188 PHE cc_start: 0.6860 (t80) cc_final: 0.6466 (t80)
REVERT: A  191 HIS cc_start: 0.7740 (p90) cc_final: 0.7352 (p90)
REVERT: A  220 LYS cc_start: 0.8359 (tptt) cc_final: 0.7977 (tptt)
REVERT: A  249 MET cc_start: 0.8614 (mmm) cc_final: 0.8252 (mmm)
REVERT: B   61 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7956 (mt)
REVERT: B  188 PHE cc_start: 0.6864 (t80) cc_final: 0.6472 (t80)
REVERT: B  191 HIS cc_start: 0.7734 (p90) cc_final: 0.7362 (p90)
REVERT: B  220 LYS cc_start: 0.8362 (tptt) cc_final: 0.7982 (tptt)
REVERT: B  249 MET cc_start: 0.8588 (mmm) cc_final: 0.8237 (mmm)
REVERT: C   61 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7959 (mt)
REVERT: C  188 PHE cc_start: 0.6851 (t80) cc_final: 0.6455 (t80)
REVERT: C  191 HIS cc_start: 0.7721 (p90) cc_final: 0.7344 (p90)
REVERT: C  220 LYS cc_start: 0.8357 (tptt) cc_final: 0.7977 (tptt)
REVERT: C  249 MET cc_start: 0.8585 (mmm) cc_final: 0.8243 (mmm)
REVERT: D   61 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7958 (mt)
REVERT: D  188 PHE cc_start: 0.6846 (t80) cc_final: 0.6454 (t80)
REVERT: D  191 HIS cc_start: 0.7731 (p90) cc_final: 0.7349 (p90)
REVERT: D  220 LYS cc_start: 0.8356 (tptt) cc_final: 0.7975 (tptt)
REVERT: D  249 MET cc_start: 0.8607 (mmm) cc_final: 0.8253 (mmm)
  outliers start: 34
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1007
  time to fit residues: 25.5774
Evaluate side-chains
  178 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  245 LEU
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  245 LEU
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 67 optimal weight:   40.0000
   chunk 54 optimal weight:    0.6980
   chunk 1 optimal weight:   30.0000
   chunk 61 optimal weight:    0.5980
   chunk 114 optimal weight:    9.9990
   chunk 24 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 129 optimal weight:    8.9990
   chunk 113 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 314 ASN
B 314 ASN
C 314 ASN
D 314 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.185035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.128027 restraints weight = 14268.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.132167 restraints weight = 8722.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.134934 restraints weight = 6352.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136583 restraints weight = 5206.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.137715 restraints weight = 4619.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10592  Z= 0.108
  Angle     :  0.520   6.024  14340  Z= 0.266
  Chirality :  0.040   0.175   1636
  Planarity :  0.004   0.041   1824
  Dihedral  :  4.258  37.211   1424
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 16.05 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.24), residues: 1312
  helix:  1.05 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.43 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 297 
 TYR   0.009   0.001   TYR D 244 
 PHE   0.013   0.001   PHE B 118 
 TRP   0.008   0.001   TRP A 196 
 HIS   0.002   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (10592)
  covalent geometry    : angle       0.52006 (14340)
  hydrogen bonds       : bond        0.03483 (  548)
  hydrogen bonds       : angle       3.77740 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 176
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7821 (mt)
REVERT: A  128 LEU cc_start: 0.5677 (tp) cc_final: 0.5193 (tp)
REVERT: A  188 PHE cc_start: 0.6682 (t80) cc_final: 0.6254 (t80)
REVERT: A  191 HIS cc_start: 0.8014 (p90) cc_final: 0.7599 (p90)
REVERT: A  220 LYS cc_start: 0.8312 (tptt) cc_final: 0.7890 (tptt)
REVERT: A  223 MET cc_start: 0.8645 (mmm) cc_final: 0.8437 (mmm)
REVERT: A  249 MET cc_start: 0.8686 (mmm) cc_final: 0.8306 (mmm)
REVERT: B   61 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7821 (mt)
REVERT: B  128 LEU cc_start: 0.5655 (tp) cc_final: 0.5172 (tp)
REVERT: B  188 PHE cc_start: 0.6683 (t80) cc_final: 0.6256 (t80)
REVERT: B  191 HIS cc_start: 0.8019 (p90) cc_final: 0.7613 (p90)
REVERT: B  220 LYS cc_start: 0.8318 (tptt) cc_final: 0.7897 (tptt)
REVERT: B  223 MET cc_start: 0.8646 (mmm) cc_final: 0.8442 (mmm)
REVERT: B  249 MET cc_start: 0.8668 (mmm) cc_final: 0.8310 (mmm)
REVERT: C   61 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7826 (mt)
REVERT: C  128 LEU cc_start: 0.5649 (tp) cc_final: 0.5166 (tp)
REVERT: C  188 PHE cc_start: 0.6683 (t80) cc_final: 0.6251 (t80)
REVERT: C  191 HIS cc_start: 0.8008 (p90) cc_final: 0.7601 (p90)
REVERT: C  220 LYS cc_start: 0.8311 (tptt) cc_final: 0.7892 (tptt)
REVERT: C  223 MET cc_start: 0.8646 (mmm) cc_final: 0.8441 (mmm)
REVERT: C  249 MET cc_start: 0.8668 (mmm) cc_final: 0.8308 (mmm)
REVERT: D   61 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7828 (mt)
REVERT: D  128 LEU cc_start: 0.5673 (tp) cc_final: 0.5188 (tp)
REVERT: D  188 PHE cc_start: 0.6675 (t80) cc_final: 0.6245 (t80)
REVERT: D  191 HIS cc_start: 0.8010 (p90) cc_final: 0.7603 (p90)
REVERT: D  220 LYS cc_start: 0.8309 (tptt) cc_final: 0.7892 (tptt)
REVERT: D  223 MET cc_start: 0.8648 (mmm) cc_final: 0.8439 (mmm)
REVERT: D  249 MET cc_start: 0.8683 (mmm) cc_final: 0.8305 (mmm)
  outliers start: 12
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1066
  time to fit residues: 27.0546
Evaluate side-chains
  172 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain D residue   61 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 83 optimal weight:   10.0000
   chunk 45 optimal weight:   50.0000
   chunk 84 optimal weight:    5.9990
   chunk 119 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 125 optimal weight:   10.0000
   chunk 47 optimal weight:    8.9990
   chunk 111 optimal weight:   40.0000
   chunk 7 optimal weight:   20.0000
   chunk 92 optimal weight:    7.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 314 ASN
B  87 HIS
B 314 ASN
C  87 HIS
C 314 ASN
D  87 HIS
D 314 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.178348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.122378 restraints weight = 14627.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125371 restraints weight = 10166.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.127325 restraints weight = 8034.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.128392 restraints weight = 6922.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.129292 restraints weight = 6335.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.4814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  10592  Z= 0.233
  Angle     :  0.625   5.479  14340  Z= 0.326
  Chirality :  0.044   0.211   1636
  Planarity :  0.005   0.049   1824
  Dihedral  :  4.238  24.513   1424
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 16.76 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.23), residues: 1312
  helix:  0.76 (0.18), residues: 820
  sheet:  None (None), residues: 0
  loop : -0.64 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 297 
 TYR   0.023   0.002   TYR A 244 
 PHE   0.010   0.002   PHE B  33 
 TRP   0.012   0.002   TRP A 196 
 HIS   0.004   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00550 (10592)
  covalent geometry    : angle       0.62461 (14340)
  hydrogen bonds       : bond        0.04465 (  548)
  hydrogen bonds       : angle       4.15728 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 172
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8021 (mt)
REVERT: A  128 LEU cc_start: 0.6533 (tp) cc_final: 0.5989 (tp)
REVERT: A  188 PHE cc_start: 0.6452 (t80) cc_final: 0.6026 (t80)
REVERT: A  191 HIS cc_start: 0.7789 (p90) cc_final: 0.7425 (p90)
REVERT: A  220 LYS cc_start: 0.8462 (tptt) cc_final: 0.8091 (tptt)
REVERT: A  249 MET cc_start: 0.8471 (mmm) cc_final: 0.8184 (mmm)
REVERT: B   61 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8023 (mt)
REVERT: B  128 LEU cc_start: 0.6533 (tp) cc_final: 0.5991 (tp)
REVERT: B  188 PHE cc_start: 0.6463 (t80) cc_final: 0.6031 (t80)
REVERT: B  191 HIS cc_start: 0.7794 (p90) cc_final: 0.7435 (p90)
REVERT: B  220 LYS cc_start: 0.8465 (tptt) cc_final: 0.8092 (tptt)
REVERT: B  249 MET cc_start: 0.8455 (mmm) cc_final: 0.8149 (mmm)
REVERT: C   61 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8026 (mt)
REVERT: C  128 LEU cc_start: 0.6547 (tp) cc_final: 0.6000 (tp)
REVERT: C  188 PHE cc_start: 0.6456 (t80) cc_final: 0.6024 (t80)
REVERT: C  191 HIS cc_start: 0.7769 (p90) cc_final: 0.7417 (p90)
REVERT: C  220 LYS cc_start: 0.8457 (tptt) cc_final: 0.8085 (tptt)
REVERT: C  249 MET cc_start: 0.8439 (mmm) cc_final: 0.8143 (mmm)
REVERT: D   61 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8024 (mt)
REVERT: D  128 LEU cc_start: 0.6542 (tp) cc_final: 0.5994 (tp)
REVERT: D  188 PHE cc_start: 0.6443 (t80) cc_final: 0.6019 (t80)
REVERT: D  191 HIS cc_start: 0.7778 (p90) cc_final: 0.7424 (p90)
REVERT: D  220 LYS cc_start: 0.8455 (tptt) cc_final: 0.8083 (tptt)
REVERT: D  244 TYR cc_start: 0.8802 (t80) cc_final: 0.8573 (t80)
REVERT: D  249 MET cc_start: 0.8455 (mmm) cc_final: 0.8179 (mmm)
  outliers start: 38
  outliers final: 26
  residues processed: 194
  average time/residue: 0.0958
  time to fit residues: 26.7055
Evaluate side-chains
  192 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 162
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   60 LEU
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   77 VAL
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 25 optimal weight:    0.9990
   chunk 10 optimal weight:   20.0000
   chunk 76 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.182126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.126445 restraints weight = 14423.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.129868 restraints weight = 9629.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.132176 restraints weight = 7405.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.133541 restraints weight = 6262.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.134514 restraints weight = 5658.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.5104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10592  Z= 0.130
  Angle     :  0.544   6.665  14340  Z= 0.276
  Chirality :  0.040   0.154   1636
  Planarity :  0.005   0.042   1824
  Dihedral  :  4.043  29.089   1424
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.46 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.23), residues: 1312
  helix:  0.93 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.57 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 297 
 TYR   0.038   0.001   TYR A 244 
 PHE   0.016   0.002   PHE A  69 
 TRP   0.010   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (10592)
  covalent geometry    : angle       0.54391 (14340)
  hydrogen bonds       : bond        0.03611 (  548)
  hydrogen bonds       : angle       3.81179 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 172
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: A   65 ARG cc_start: 0.8598 (mmm160) cc_final: 0.8398 (mmm160)
REVERT: A  188 PHE cc_start: 0.6417 (t80) cc_final: 0.5902 (t80)
REVERT: A  191 HIS cc_start: 0.7758 (p90) cc_final: 0.7372 (p90)
REVERT: A  220 LYS cc_start: 0.8399 (tptt) cc_final: 0.8039 (tptt)
REVERT: A  249 MET cc_start: 0.8476 (mmm) cc_final: 0.8029 (mmm)
REVERT: B   61 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8010 (mt)
REVERT: B   65 ARG cc_start: 0.8605 (mmm160) cc_final: 0.8403 (mmm160)
REVERT: B  128 LEU cc_start: 0.6433 (tp) cc_final: 0.6201 (tp)
REVERT: B  188 PHE cc_start: 0.6421 (t80) cc_final: 0.5916 (t80)
REVERT: B  191 HIS cc_start: 0.7728 (p90) cc_final: 0.6742 (p90)
REVERT: B  195 ASP cc_start: 0.8263 (m-30) cc_final: 0.7974 (m-30)
REVERT: B  220 LYS cc_start: 0.8399 (tptt) cc_final: 0.8025 (tptt)
REVERT: B  249 MET cc_start: 0.8472 (mmm) cc_final: 0.8037 (mmm)
REVERT: C   61 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8018 (mt)
REVERT: C   65 ARG cc_start: 0.8599 (mmm160) cc_final: 0.8395 (mmm160)
REVERT: C  128 LEU cc_start: 0.6431 (tp) cc_final: 0.6190 (tp)
REVERT: C  188 PHE cc_start: 0.6414 (t80) cc_final: 0.5911 (t80)
REVERT: C  191 HIS cc_start: 0.7741 (p90) cc_final: 0.6783 (p90)
REVERT: C  195 ASP cc_start: 0.8251 (m-30) cc_final: 0.7968 (m-30)
REVERT: C  220 LYS cc_start: 0.8392 (tptt) cc_final: 0.8025 (tptt)
REVERT: C  249 MET cc_start: 0.8464 (mmm) cc_final: 0.8059 (mmm)
REVERT: D   61 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8021 (mt)
REVERT: D   65 ARG cc_start: 0.8597 (mmm160) cc_final: 0.8395 (mmm160)
REVERT: D  128 LEU cc_start: 0.6438 (tp) cc_final: 0.6200 (tp)
REVERT: D  188 PHE cc_start: 0.6406 (t80) cc_final: 0.5897 (t80)
REVERT: D  191 HIS cc_start: 0.7748 (p90) cc_final: 0.7379 (p90)
REVERT: D  220 LYS cc_start: 0.8392 (tptt) cc_final: 0.8030 (tptt)
REVERT: D  244 TYR cc_start: 0.8808 (t80) cc_final: 0.8555 (t80)
REVERT: D  249 MET cc_start: 0.8490 (mmm) cc_final: 0.8175 (mmm)
  outliers start: 29
  outliers final: 13
  residues processed: 189
  average time/residue: 0.1036
  time to fit residues: 27.5019
Evaluate side-chains
  177 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 66 optimal weight:   20.0000
   chunk 39 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   chunk 48 optimal weight:   20.0000
   chunk 47 optimal weight:    0.6980
   chunk 101 optimal weight:   30.0000
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   chunk 108 optimal weight:    0.2980
   chunk 60 optimal weight:   10.0000
   chunk 13 optimal weight:   20.0000
   overall best weight:    5.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.191521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.135940 restraints weight = 15915.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.141034 restraints weight = 8675.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.144254 restraints weight = 5904.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.146170 restraints weight = 4671.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.147507 restraints weight = 4063.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10592  Z= 0.215
  Angle     :  0.629   6.787  14340  Z= 0.323
  Chirality :  0.043   0.174   1636
  Planarity :  0.006   0.058   1824
  Dihedral  :  4.131  23.087   1424
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.93 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.23), residues: 1312
  helix:  0.74 (0.18), residues: 812
  sheet:  None (None), residues: 0
  loop : -0.59 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 297 
 TYR   0.017   0.002   TYR D 244 
 PHE   0.010   0.002   PHE A  33 
 TRP   0.011   0.002   TRP A 196 
 HIS   0.005   0.001   HIS B 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (10592)
  covalent geometry    : angle       0.62926 (14340)
  hydrogen bonds       : bond        0.04220 (  548)
  hydrogen bonds       : angle       4.04542 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8051 (mt)
REVERT: A   65 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8543 (mmm160)
REVERT: A  188 PHE cc_start: 0.6425 (t80) cc_final: 0.5804 (t80)
REVERT: A  191 HIS cc_start: 0.8032 (p90) cc_final: 0.7581 (p90)
REVERT: A  220 LYS cc_start: 0.8304 (tptt) cc_final: 0.7978 (tptt)
REVERT: A  249 MET cc_start: 0.8715 (mmm) cc_final: 0.8164 (mmm)
REVERT: B   61 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8035 (mt)
REVERT: B   65 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8539 (mmm160)
REVERT: B  128 LEU cc_start: 0.6934 (tp) cc_final: 0.6709 (tp)
REVERT: B  188 PHE cc_start: 0.6432 (t80) cc_final: 0.5810 (t80)
REVERT: B  191 HIS cc_start: 0.8037 (p90) cc_final: 0.7588 (p90)
REVERT: B  220 LYS cc_start: 0.8311 (tptt) cc_final: 0.7986 (tptt)
REVERT: B  249 MET cc_start: 0.8710 (mmm) cc_final: 0.8270 (mmm)
REVERT: C   61 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8038 (mt)
REVERT: C   65 ARG cc_start: 0.8886 (mmm160) cc_final: 0.8544 (mmm160)
REVERT: C  128 LEU cc_start: 0.6926 (tp) cc_final: 0.6700 (tp)
REVERT: C  188 PHE cc_start: 0.6425 (t80) cc_final: 0.5802 (t80)
REVERT: C  191 HIS cc_start: 0.8023 (p90) cc_final: 0.7580 (p90)
REVERT: C  220 LYS cc_start: 0.8301 (tptt) cc_final: 0.7977 (tptt)
REVERT: C  249 MET cc_start: 0.8709 (mmm) cc_final: 0.8277 (mmm)
REVERT: D   61 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8035 (mt)
REVERT: D   65 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8548 (mmm160)
REVERT: D  128 LEU cc_start: 0.6929 (tp) cc_final: 0.6705 (tp)
REVERT: D  188 PHE cc_start: 0.6416 (t80) cc_final: 0.5791 (t80)
REVERT: D  191 HIS cc_start: 0.8028 (p90) cc_final: 0.7581 (p90)
REVERT: D  220 LYS cc_start: 0.8307 (tptt) cc_final: 0.7980 (tptt)
REVERT: D  249 MET cc_start: 0.8725 (mmm) cc_final: 0.8293 (mmm)
  outliers start: 29
  outliers final: 17
  residues processed: 183
  average time/residue: 0.1058
  time to fit residues: 27.5057
Evaluate side-chains
  175 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  364 ILE
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  148 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  148 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 0 optimal weight:   20.0000
   chunk 47 optimal weight:    9.9990
   chunk 108 optimal weight:    0.0870
   chunk 36 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 115 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0570
   chunk 118 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    2.0080

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
B 198 ASN
C 198 ASN
D 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.217971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153117 restraints weight = 16599.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.158029 restraints weight = 9406.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.161587 restraints weight = 6522.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.163721 restraints weight = 5184.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.165209 restraints weight = 4496.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.5369

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10592  Z= 0.117
  Angle     :  0.568   7.409  14340  Z= 0.280
  Chirality :  0.039   0.168   1636
  Planarity :  0.005   0.056   1824
  Dihedral  :  3.891  26.663   1424
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.20 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.23), residues: 1312
  helix:  0.95 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.52 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 297 
 TYR   0.024   0.001   TYR C 244 
 PHE   0.008   0.001   PHE A  33 
 TRP   0.010   0.001   TRP C 196 
 HIS   0.002   0.000   HIS C  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10592)
  covalent geometry    : angle       0.56771 (14340)
  hydrogen bonds       : bond        0.03425 (  548)
  hydrogen bonds       : angle       3.76222 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8104 (mt)
REVERT: A   65 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8482 (mmm160)
REVERT: A  188 PHE cc_start: 0.6312 (t80) cc_final: 0.5701 (t80)
REVERT: A  220 LYS cc_start: 0.8166 (tptt) cc_final: 0.7588 (tptt)
REVERT: A  249 MET cc_start: 0.8661 (mmm) cc_final: 0.8092 (mmm)
REVERT: B   61 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8097 (mt)
REVERT: B   65 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8483 (mmm160)
REVERT: B  128 LEU cc_start: 0.6887 (tp) cc_final: 0.6657 (tp)
REVERT: B  188 PHE cc_start: 0.6316 (t80) cc_final: 0.5707 (t80)
REVERT: B  195 ASP cc_start: 0.8468 (m-30) cc_final: 0.8083 (m-30)
REVERT: B  220 LYS cc_start: 0.8167 (tptt) cc_final: 0.7652 (tptt)
REVERT: B  249 MET cc_start: 0.8658 (mmm) cc_final: 0.8097 (mmm)
REVERT: C   61 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8099 (mt)
REVERT: C   65 ARG cc_start: 0.8922 (mmm160) cc_final: 0.8483 (mmm160)
REVERT: C  128 LEU cc_start: 0.6878 (tp) cc_final: 0.6645 (tp)
REVERT: C  188 PHE cc_start: 0.6309 (t80) cc_final: 0.5696 (t80)
REVERT: C  195 ASP cc_start: 0.8465 (m-30) cc_final: 0.8082 (m-30)
REVERT: C  220 LYS cc_start: 0.8158 (tptt) cc_final: 0.7648 (tptt)
REVERT: C  249 MET cc_start: 0.8658 (mmm) cc_final: 0.8100 (mmm)
REVERT: D   61 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8089 (mt)
REVERT: D   65 ARG cc_start: 0.8930 (mmm160) cc_final: 0.8488 (mmm160)
REVERT: D  128 LEU cc_start: 0.6897 (tp) cc_final: 0.6661 (tp)
REVERT: D  188 PHE cc_start: 0.6292 (t80) cc_final: 0.5674 (t80)
REVERT: D  220 LYS cc_start: 0.8162 (tptt) cc_final: 0.7583 (tptt)
REVERT: D  244 TYR cc_start: 0.9092 (t80) cc_final: 0.8779 (t80)
REVERT: D  249 MET cc_start: 0.8683 (mmm) cc_final: 0.8145 (mmm)
  outliers start: 22
  outliers final: 14
  residues processed: 198
  average time/residue: 0.1017
  time to fit residues: 28.5674
Evaluate side-chains
  186 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 121 optimal weight:    0.8980
   chunk 10 optimal weight:   30.0000
   chunk 7 optimal weight:   40.0000
   chunk 36 optimal weight:    8.9990
   chunk 12 optimal weight:   50.0000
   chunk 129 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 110 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
B 198 ASN
C 198 ASN
D 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.217260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.153158 restraints weight = 16414.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.158376 restraints weight = 9206.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.161832 restraints weight = 6334.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.164004 restraints weight = 5021.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.165589 restraints weight = 4342.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10592  Z= 0.117
  Angle     :  0.576   7.622  14340  Z= 0.284
  Chirality :  0.040   0.150   1636
  Planarity :  0.005   0.058   1824
  Dihedral  :  3.842  26.026   1424
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.09 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.23), residues: 1312
  helix:  1.07 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.42 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 297 
 TYR   0.021   0.001   TYR C 244 
 PHE   0.009   0.001   PHE A 118 
 TRP   0.040   0.004   TRP C 196 
 HIS   0.002   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10592)
  covalent geometry    : angle       0.57619 (14340)
  hydrogen bonds       : bond        0.03345 (  548)
  hydrogen bonds       : angle       3.67466 ( 1560)

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

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

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2624 Ramachandran restraints generated.
    1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 173
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8097 (mt)
REVERT: A   65 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8498 (mmm160)
REVERT: A  170 MET cc_start: 0.6273 (mmp) cc_final: 0.6038 (mmt)
REVERT: A  188 PHE cc_start: 0.6250 (t80) cc_final: 0.5648 (t80)
REVERT: A  191 HIS cc_start: 0.8460 (p90) cc_final: 0.7718 (p90)
REVERT: A  220 LYS cc_start: 0.8256 (tptt) cc_final: 0.7850 (tptt)
REVERT: A  221 GLU cc_start: 0.8100 (mp0) cc_final: 0.7769 (mp0)
REVERT: A  249 MET cc_start: 0.8643 (mmm) cc_final: 0.8107 (mmm)
REVERT: B   61 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8089 (mt)
REVERT: B  128 LEU cc_start: 0.7008 (tp) cc_final: 0.6780 (tp)
REVERT: B  170 MET cc_start: 0.6280 (mmp) cc_final: 0.6044 (mmt)
REVERT: B  188 PHE cc_start: 0.6249 (t80) cc_final: 0.5655 (t80)
REVERT: B  191 HIS cc_start: 0.8460 (p90) cc_final: 0.7280 (p90)
REVERT: B  220 LYS cc_start: 0.8262 (tptt) cc_final: 0.7850 (tptt)
REVERT: B  221 GLU cc_start: 0.8111 (mp0) cc_final: 0.7776 (mp0)
REVERT: B  249 MET cc_start: 0.8588 (mmm) cc_final: 0.8069 (mmm)
REVERT: C   61 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8089 (mt)
REVERT: C  128 LEU cc_start: 0.7002 (tp) cc_final: 0.6772 (tp)
REVERT: C  170 MET cc_start: 0.6279 (mmp) cc_final: 0.6038 (mmt)
REVERT: C  188 PHE cc_start: 0.6240 (t80) cc_final: 0.5636 (t80)
REVERT: C  191 HIS cc_start: 0.8460 (p90) cc_final: 0.7281 (p90)
REVERT: C  220 LYS cc_start: 0.8260 (tptt) cc_final: 0.7857 (tptt)
REVERT: C  221 GLU cc_start: 0.8097 (mp0) cc_final: 0.7769 (mp0)
REVERT: C  249 MET cc_start: 0.8585 (mmm) cc_final: 0.8071 (mmm)
REVERT: D   61 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8078 (mt)
REVERT: D   65 ARG cc_start: 0.8908 (mmm160) cc_final: 0.8506 (mmm160)
REVERT: D  128 LEU cc_start: 0.7019 (tp) cc_final: 0.6785 (tp)
REVERT: D  170 MET cc_start: 0.6270 (mmp) cc_final: 0.6032 (mmt)
REVERT: D  188 PHE cc_start: 0.6225 (t80) cc_final: 0.5616 (t80)
REVERT: D  191 HIS cc_start: 0.8459 (p90) cc_final: 0.7724 (p90)
REVERT: D  220 LYS cc_start: 0.8261 (tptt) cc_final: 0.7851 (tptt)
REVERT: D  221 GLU cc_start: 0.8101 (mp0) cc_final: 0.7765 (mp0)
REVERT: D  244 TYR cc_start: 0.9077 (t80) cc_final: 0.8711 (t80)
REVERT: D  249 MET cc_start: 0.8636 (mmm) cc_final: 0.8122 (mmm)
  outliers start: 26
  outliers final: 14
  residues processed: 191
  average time/residue: 0.0994
  time to fit residues: 27.2958
Evaluate side-chains
  176 residues out of total 1128 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   95 VAL
Chi-restraints excluded: chain A residue  113 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue   61 LEU
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  113 VAL
Chi-restraints excluded: chain B residue  364 ILE
Chi-restraints excluded: chain C residue   60 LEU
Chi-restraints excluded: chain C residue   61 LEU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  364 ILE
Chi-restraints excluded: chain D residue   61 LEU
Chi-restraints excluded: chain D residue   95 VAL
Chi-restraints excluded: chain D residue  113 VAL
Chi-restraints excluded: chain D residue  245 LEU
Chi-restraints excluded: chain D residue  364 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 118 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 79 optimal weight:    8.9990
   chunk 66 optimal weight:   20.0000
   chunk 98 optimal weight:    0.0050
   chunk 92 optimal weight:    5.9990
   chunk 13 optimal weight:   20.0000
   overall best weight:    2.6000

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

Flipped N/Q/H residues before XYZ refinement:
A 198 ASN
B 198 ASN
C 198 ASN
D 198 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.215209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.151939 restraints weight = 16575.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.157149 restraints weight = 9288.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.160604 restraints weight = 6401.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.162726 restraints weight = 5060.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.164214 restraints weight = 4369.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.5590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10592  Z= 0.133
  Angle     :  0.596   7.528  14340  Z= 0.294
  Chirality :  0.040   0.150   1636
  Planarity :  0.005   0.058   1824
  Dihedral  :  3.830  25.730   1424
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.33 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.23), residues: 1312
  helix:  1.00 (0.18), residues: 832
  sheet:  None (None), residues: 0
  loop : -0.37 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D 346 
 TYR   0.020   0.001   TYR B 244 
 PHE   0.010   0.001   PHE A 118 
 TRP   0.039   0.003   TRP D 196 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10592)
  covalent geometry    : angle       0.59642 (14340)
  hydrogen bonds       : bond        0.03449 (  548)
  hydrogen bonds       : angle       3.74790 ( 1560)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1822.36 seconds
wall clock time: 32 minutes 14.33 seconds (1934.33 seconds total)