Starting phenix.real_space_refine
on Wed Feb 12 14:42:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y1x_38849/02_2025/8y1x_38849.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.004 sd=   0.037
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      28      5.16       5
     C    5294      2.51       5
     N    1284      2.21       5
     O    1468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8074
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4028
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4028
          Classifications: {'peptide': 543}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 18, 'TRANS': 524}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.39, per 1000 atoms: 0.79
  Number of scatterers: 8074
  At special positions: 0
  Unit cell: (108.979, 81.1008, 109.824, 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      28     16.00
     O    1468      8.00
     N    1284      7.00
     C    5294      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: 1.98
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1968

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 10 sheets defined
      69.9% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 11
      removed outlier: 4.142A  pdb=" N   GLY A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 19
    Processing helix  chain 'A' and resid 20 through 29
      removed outlier: 4.098A  pdb=" N   TYR A  24 " --> pdb=" O   LEU A  20 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 50
    Processing helix  chain 'A' and resid 58 through 88
      removed outlier: 3.796A  pdb=" N   GLY A  62 " --> pdb=" O   ASP A  58 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      Proline residue:  A  79  - end of helix
      removed outlier: 4.199A  pdb=" N   ILE A  82 " --> pdb=" O   GLY A  78 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   SER A  83 " --> pdb=" O   PRO A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 115
    Processing helix  chain 'A' and resid 117 through 129
    Processing helix  chain 'A' and resid 132 through 145
      removed outlier: 4.365A  pdb=" N   GLY A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 180
      removed outlier: 3.748A  pdb=" N   ILE A 159 " --> pdb=" O   TYR A 155 " (cutoff:3.500A)
      Proline residue:  A 160  - end of helix
      removed outlier: 3.903A  pdb=" N   VAL A 168 " --> pdb=" O   THR A 164 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   PHE A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR A 171 " --> pdb=" O   TYR A 167 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 187
    Processing helix  chain 'A' and resid 189 through 201
      removed outlier: 3.559A  pdb=" N   ALA A 194 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 236
    Processing helix  chain 'A' and resid 266 through 277
    Processing helix  chain 'A' and resid 302 through 312
    Processing helix  chain 'A' and resid 324 through 329
      removed outlier: 3.712A  pdb=" N   SER A 329 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 354
    Processing helix  chain 'A' and resid 364 through 381
      removed outlier: 3.779A  pdb=" N   VAL A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 412
      removed outlier: 3.616A  pdb=" N   SER A 398 " --> pdb=" O   GLY A 394 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 400 " --> pdb=" O   THR A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 442
      removed outlier: 3.717A  pdb=" N   LEU A 423 " --> pdb=" O   PRO A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 453
    Processing helix  chain 'A' and resid 458 through 478
      Proline residue:  A 468  - end of helix
    Processing helix  chain 'A' and resid 483 through 495
      removed outlier: 3.735A  pdb=" N   ILE A 487 " --> pdb=" O   GLU A 483 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE A 488 " --> pdb=" O   PRO A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 509
      removed outlier: 3.616A  pdb=" N   GLY A 509 " --> pdb=" O   SER A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 543
      removed outlier: 3.672A  pdb=" N   ALA A 518 " --> pdb=" O   PRO A 514 " (cutoff:3.500A)
      Proline residue:  A 522  - end of helix
      removed outlier: 4.217A  pdb=" N   ALA A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY A 535 " --> pdb=" O   LEU A 531 " (cutoff:3.500A)
      Proline residue:  A 536  - end of helix
    Processing helix  chain 'B' and resid 2 through 11
    Processing helix  chain 'B' and resid 11 through 19
    Processing helix  chain 'B' and resid 20 through 29
      removed outlier: 4.097A  pdb=" N   TYR B  24 " --> pdb=" O   LEU B  20 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 37 through 50
    Processing helix  chain 'B' and resid 58 through 88
      removed outlier: 3.795A  pdb=" N   GLY B  62 " --> pdb=" O   ASP B  58 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE B  69 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      Proline residue:  B  79  - end of helix
      removed outlier: 4.199A  pdb=" N   ILE B  82 " --> pdb=" O   GLY B  78 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   SER B  83 " --> pdb=" O   PRO B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 115
    Processing helix  chain 'B' and resid 117 through 129
    Processing helix  chain 'B' and resid 132 through 145
      removed outlier: 4.365A  pdb=" N   GLY B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 180
      removed outlier: 3.748A  pdb=" N   ILE B 159 " --> pdb=" O   TYR B 155 " (cutoff:3.500A)
      Proline residue:  B 160  - end of helix
      removed outlier: 3.903A  pdb=" N   VAL B 168 " --> pdb=" O   THR B 164 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   PHE B 169 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   THR B 171 " --> pdb=" O   TYR B 167 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ILE B 172 " --> pdb=" O   VAL B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 187
    Processing helix  chain 'B' and resid 189 through 201
      removed outlier: 3.560A  pdb=" N   ALA B 194 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 236
    Processing helix  chain 'B' and resid 266 through 277
    Processing helix  chain 'B' and resid 302 through 312
    Processing helix  chain 'B' and resid 324 through 329
      removed outlier: 3.712A  pdb=" N   SER B 329 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 344 through 354
    Processing helix  chain 'B' and resid 364 through 381
      removed outlier: 3.779A  pdb=" N   VAL B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 412
      removed outlier: 3.615A  pdb=" N   SER B 398 " --> pdb=" O   GLY B 394 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE B 400 " --> pdb=" O   THR B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 442
      removed outlier: 3.718A  pdb=" N   LEU B 423 " --> pdb=" O   PRO B 419 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 445 through 453
    Processing helix  chain 'B' and resid 458 through 478
      Proline residue:  B 468  - end of helix
    Processing helix  chain 'B' and resid 483 through 495
      removed outlier: 3.736A  pdb=" N   ILE B 487 " --> pdb=" O   GLU B 483 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ILE B 488 " --> pdb=" O   PRO B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 509
      removed outlier: 3.616A  pdb=" N   GLY B 509 " --> pdb=" O   SER B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 543
      removed outlier: 3.672A  pdb=" N   ALA B 518 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
      Proline residue:  B 522  - end of helix
      removed outlier: 4.217A  pdb=" N   ALA B 525 " --> pdb=" O   ALA B 521 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   ILE B 526 " --> pdb=" O   PRO B 522 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLY B 535 " --> pdb=" O   LEU B 531 " (cutoff:3.500A)
      Proline residue:  B 536  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31
      removed outlier: 3.687A  pdb=" N   ILE A  31 " --> pdb=" O   PHE A  34 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 214
      removed outlier: 3.656A  pdb=" N   SER A 212 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLY A 265 " --> pdb=" O   SER A 212 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217
    Processing sheet with id=AA4, first strand: chain 'A' and resid 292 through 294
      removed outlier: 3.637A  pdb=" N   VAL A 340 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 314 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 382 through 385
    Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 31
      removed outlier: 3.687A  pdb=" N   ILE B  31 " --> pdb=" O   PHE B  34 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 212 through 214
      removed outlier: 3.656A  pdb=" N   SER B 212 " --> pdb=" O   GLY B 265 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   GLY B 265 " --> pdb=" O   SER B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 216 through 217
    Processing sheet with id=AA9, first strand: chain 'B' and resid 292 through 294
      removed outlier: 3.637A  pdb=" N   VAL B 340 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 314 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 382 through 385

    522 hydrogen bonds defined for protein.
    1512 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: 2.71

  Time building geometry restraints manager: 2.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2508
        1.34 -     1.46: 1217
        1.46 -     1.57: 4437
        1.57 -     1.69: 0
        1.69 -     1.80: 56
  Bond restraints: 8218
  Sorted by residual:
  bond pdb=" CA  SER B 513 "
       pdb=" CB  SER B 513 "
    ideal  model  delta    sigma   weight residual
    1.533  1.493  0.040 1.39e-02 5.18e+03 8.34e+00
  bond pdb=" CA  SER A 513 "
       pdb=" CB  SER A 513 "
    ideal  model  delta    sigma   weight residual
    1.533  1.493  0.040 1.39e-02 5.18e+03 8.24e+00
  bond pdb=" N   PHE B 515 "
       pdb=" CA  PHE B 515 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.030 1.27e-02 6.20e+03 5.44e+00
  bond pdb=" N   SER A 513 "
       pdb=" CA  SER A 513 "
    ideal  model  delta    sigma   weight residual
    1.459  1.483 -0.024 1.04e-02 9.25e+03 5.26e+00
  bond pdb=" N   PHE A 515 "
       pdb=" CA  PHE A 515 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.27e-02 6.20e+03 5.25e+00
  ... (remaining 8213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.14: 11002
        2.14 -     4.29: 128
        4.29 -     6.43: 26
        6.43 -     8.57: 4
        8.57 -    10.71: 2
  Bond angle restraints: 11162
  Sorted by residual:
  angle pdb=" N   PHE B 515 "
        pdb=" CA  PHE B 515 "
        pdb=" C   PHE B 515 "
      ideal   model   delta    sigma   weight residual
     112.04  107.05    4.99 1.44e+00 4.82e-01 1.20e+01
  angle pdb=" N   PHE A 515 "
        pdb=" CA  PHE A 515 "
        pdb=" C   PHE A 515 "
      ideal   model   delta    sigma   weight residual
     112.04  107.08    4.96 1.44e+00 4.82e-01 1.19e+01
  angle pdb=" N   GLY A  78 "
        pdb=" CA  GLY A  78 "
        pdb=" C   GLY A  78 "
      ideal   model   delta    sigma   weight residual
     112.34  118.62   -6.28 2.04e+00 2.40e-01 9.49e+00
  angle pdb=" N   GLY B  78 "
        pdb=" CA  GLY B  78 "
        pdb=" C   GLY B  78 "
      ideal   model   delta    sigma   weight residual
     112.34  118.61   -6.27 2.04e+00 2.40e-01 9.45e+00
  angle pdb=" CA  LEU A 280 "
        pdb=" CB  LEU A 280 "
        pdb=" CG  LEU A 280 "
      ideal   model   delta    sigma   weight residual
     116.30  127.01  -10.71 3.50e+00 8.16e-02 9.37e+00
  ... (remaining 11157 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.81: 4003
       12.81 -    25.62: 499
       25.62 -    38.43: 240
       38.43 -    51.24: 80
       51.24 -    64.05: 22
  Dihedral angle restraints: 4844
    sinusoidal: 1764
      harmonic: 3080
  Sorted by residual:
  dihedral pdb=" CA  LEU B 129 "
           pdb=" C   LEU B 129 "
           pdb=" N   THR B 130 "
           pdb=" CA  THR B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  LEU A 129 "
           pdb=" C   LEU A 129 "
           pdb=" N   THR A 130 "
           pdb=" CA  THR A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  THR B 217 "
           pdb=" C   THR B 217 "
           pdb=" N   ILE B 218 "
           pdb=" CA  ILE B 218 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.56  -15.44     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 4841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 929
       0.038 -    0.077: 312
       0.077 -    0.115: 114
       0.115 -    0.153: 23
       0.153 -    0.191: 8
  Chirality restraints: 1386
  Sorted by residual:
  chirality pdb=" CG  LEU B 280 "
            pdb=" CB  LEU B 280 "
            pdb=" CD1 LEU B 280 "
            pdb=" CD2 LEU B 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CG  LEU A 280 "
            pdb=" CB  LEU A 280 "
            pdb=" CD1 LEU A 280 "
            pdb=" CD2 LEU A 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.98e-01
  chirality pdb=" CB  THR A 153 "
            pdb=" CA  THR A 153 "
            pdb=" OG1 THR A 153 "
            pdb=" CG2 THR A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.18 2.00e-01 2.50e+01 7.92e-01
  ... (remaining 1383 not shown)

  Planarity restraints: 1382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 455 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.32e+00
        pdb=" C   ILE A 455 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 455 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 456 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 455 "    0.010 2.00e-02 2.50e+03   2.07e-02 4.27e+00
        pdb=" C   ILE B 455 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ILE B 455 "    0.013 2.00e-02 2.50e+03
        pdb=" N   SER B 456 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 427 "    0.006 2.00e-02 2.50e+03   1.16e-02 1.34e+00
        pdb=" C   GLN B 427 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   GLN B 427 "    0.007 2.00e-02 2.50e+03
        pdb=" N   SER B 428 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1379 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2228
        2.81 -     3.33: 8094
        3.33 -     3.86: 12905
        3.86 -     4.38: 13929
        4.38 -     4.90: 25122
  Nonbonded interactions: 62278
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 268 "
            pdb=" NH1 ARG B 272 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" OD1 ASP A 268 "
            pdb=" NH1 ARG A 272 "
     model   vdw
     2.289 3.120
  nonbonded pdb=" OG1 THR B 217 "
            pdb=" O   GLY B 258 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG1 THR A 217 "
            pdb=" O   GLY A 258 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" OG  SER A  84 "
            pdb=" O   ALA A 518 "
     model   vdw
     2.361 3.040
  ... (remaining 62273 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.550
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     23.420
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8218  Z= 0.202
  Angle     :  0.650  10.714  11162  Z= 0.347
  Chirality :  0.046   0.191   1386
  Planarity :  0.004   0.027   1382
  Dihedral  : 15.439  64.045   2876
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 25.75 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1082
  helix:  1.24 (0.20), residues: 720
  sheet: -2.40 (0.55), residues: 62
  loop : -1.43 (0.30), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 367 
 HIS   0.001   0.000   HIS B 187 
 PHE   0.014   0.001   PHE B 169 
 TYR   0.011   0.001   TYR A 289 
 ARG   0.006   0.001   ARG A 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 VAL cc_start: 0.9588 (t) cc_final: 0.8955 (p)
REVERT: B  216 TYR cc_start: 0.7502 (m-80) cc_final: 0.6761 (m-80)
REVERT: B  251 MET cc_start: 0.7954 (mmt) cc_final: 0.7681 (mmp)
REVERT: B  315 VAL cc_start: 0.8761 (m) cc_final: 0.8499 (p)
REVERT: B  323 MET cc_start: 0.7558 (ppp) cc_final: 0.7234 (ppp)
  outliers start: 4
  outliers final: 2
  residues processed: 215
  average time/residue: 0.1787
  time to fit residues: 53.5015
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain B residue   55 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.9990
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
A 412 HIS
A 427 GLN
** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.055430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.040611 restraints weight = 40886.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.042024 restraints weight = 23384.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.042980 restraints weight = 15852.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8218  Z= 0.189
  Angle     :  0.645  10.211  11162  Z= 0.322
  Chirality :  0.044   0.201   1386
  Planarity :  0.004   0.034   1382
  Dihedral  :  4.530  39.086   1136
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 27.61 %
    Favored  : 67.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.26), residues: 1082
  helix:  1.41 (0.20), residues: 738
  sheet: -2.30 (0.58), residues: 62
  loop : -1.48 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 367 
 HIS   0.004   0.001   HIS A 414 
 PHE   0.017   0.002   PHE A 236 
 TYR   0.018   0.001   TYR A 163 
 ARG   0.004   0.001   ARG B 272 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 120
  time to evaluate  : 0.963 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  140 GLU cc_start: 0.9184 (tp30) cc_final: 0.8914 (tp30)
REVERT: A  182 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9123 (tmm)
REVERT: A  269 GLU cc_start: 0.9515 (mp0) cc_final: 0.9286 (mp0)
REVERT: A  323 MET cc_start: 0.8467 (ppp) cc_final: 0.7141 (ppp)
REVERT: A  380 ILE cc_start: 0.7719 (mm) cc_final: 0.7515 (mm)
REVERT: A  431 LEU cc_start: 0.9419 (tp) cc_final: 0.8980 (mt)
REVERT: A  480 MET cc_start: 0.9245 (ttm) cc_final: 0.8680 (ptm)
REVERT: A  541 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8967 (mm)
REVERT: B  131 GLN cc_start: 0.9187 (tm-30) cc_final: 0.8822 (tm-30)
REVERT: B  213 THR cc_start: 0.9243 (p) cc_final: 0.9017 (t)
REVERT: B  216 TYR cc_start: 0.9303 (m-80) cc_final: 0.8950 (m-80)
REVERT: B  241 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8954 (p)
REVERT: B  269 GLU cc_start: 0.9442 (mp0) cc_final: 0.9239 (mp0)
REVERT: B  323 MET cc_start: 0.8677 (ppp) cc_final: 0.7976 (ppp)
REVERT: B  339 LEU cc_start: 0.9795 (mt) cc_final: 0.9248 (pt)
REVERT: B  531 LEU cc_start: 0.9556 (tp) cc_final: 0.9311 (tp)
  outliers start: 44
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1530
  time to fit residues: 34.3302
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue  132 SER
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  435 ILE
Chi-restraints excluded: chain B residue  480 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    0.0970
   chunk 85 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 94 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.5582

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

Flipped N/Q/H residues before XYZ refinement:
B 412 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.055035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.040407 restraints weight = 41591.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.041854 restraints weight = 23204.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.042911 restraints weight = 15691.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8218  Z= 0.188
  Angle     :  0.646  13.123  11162  Z= 0.308
  Chirality :  0.043   0.163   1386
  Planarity :  0.003   0.030   1382
  Dihedral  :  4.304  41.410   1136
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 27.73 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1082
  helix:  1.62 (0.20), residues: 734
  sheet: -2.08 (0.59), residues: 62
  loop : -1.52 (0.32), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 367 
 HIS   0.002   0.001   HIS B 150 
 PHE   0.015   0.001   PHE A 300 
 TYR   0.018   0.001   TYR A 163 
 ARG   0.003   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 102
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.9549 (tpp) cc_final: 0.9197 (mpp)
REVERT: A  140 GLU cc_start: 0.9147 (tp30) cc_final: 0.8816 (tp30)
REVERT: A  182 MET cc_start: 0.9487 (tpp) cc_final: 0.9183 (tmm)
REVERT: A  380 ILE cc_start: 0.7675 (mm) cc_final: 0.7460 (mm)
REVERT: A  431 LEU cc_start: 0.9450 (tp) cc_final: 0.9087 (mt)
REVERT: A  480 MET cc_start: 0.9308 (ttm) cc_final: 0.8798 (ptm)
REVERT: A  541 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8982 (mm)
REVERT: B  131 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8863 (tm-30)
REVERT: B  140 GLU cc_start: 0.9154 (tp30) cc_final: 0.8910 (tp30)
REVERT: B  241 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9149 (p)
REVERT: B  323 MET cc_start: 0.8784 (ppp) cc_final: 0.7761 (ppp)
REVERT: B  339 LEU cc_start: 0.9763 (mt) cc_final: 0.9209 (pt)
  outliers start: 42
  outliers final: 21
  residues processed: 138
  average time/residue: 0.1420
  time to fit residues: 29.9798
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 ILE
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  480 MET
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0980
   chunk 31 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 39 optimal weight:    9.9990
   chunk 56 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 29 optimal weight:   20.0000
   chunk 2 optimal weight:    6.9990
   chunk 3 optimal weight:    0.1980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B   2 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.054583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.040012 restraints weight = 41123.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.041420 restraints weight = 22968.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.042475 restraints weight = 15605.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8218  Z= 0.180
  Angle     :  0.650  11.597  11162  Z= 0.308
  Chirality :  0.042   0.141   1386
  Planarity :  0.003   0.036   1382
  Dihedral  :  4.268  43.449   1136
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.89 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1082
  helix:  1.72 (0.20), residues: 738
  sheet: -1.94 (0.60), residues: 62
  loop : -1.54 (0.32), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 367 
 HIS   0.002   0.001   HIS B 150 
 PHE   0.024   0.001   PHE B 516 
 TYR   0.011   0.001   TYR B 216 
 ARG   0.003   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 100
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.9569 (tpp) cc_final: 0.9168 (mpp)
REVERT: A   80 SER cc_start: 0.9690 (m) cc_final: 0.9265 (t)
REVERT: A  140 GLU cc_start: 0.9151 (tp30) cc_final: 0.8788 (tp30)
REVERT: A  182 MET cc_start: 0.9457 (tpp) cc_final: 0.9157 (tmm)
REVERT: A  186 MET cc_start: 0.9233 (mmm) cc_final: 0.8573 (mmm)
REVERT: A  269 GLU cc_start: 0.9544 (mp0) cc_final: 0.9335 (mp0)
REVERT: A  323 MET cc_start: 0.8891 (ppp) cc_final: 0.7755 (ppp)
REVERT: A  380 ILE cc_start: 0.7684 (mm) cc_final: 0.7434 (mm)
REVERT: A  431 LEU cc_start: 0.9460 (tp) cc_final: 0.9096 (mt)
REVERT: A  480 MET cc_start: 0.9322 (ttm) cc_final: 0.8806 (ptm)
REVERT: A  541 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: B    2 ASN cc_start: 0.9319 (OUTLIER) cc_final: 0.9107 (t0)
REVERT: B   48 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9473 (mm)
REVERT: B  131 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8888 (tm-30)
REVERT: B  140 GLU cc_start: 0.9164 (tp30) cc_final: 0.8873 (tp30)
REVERT: B  182 MET cc_start: 0.9499 (tmm) cc_final: 0.9244 (tmm)
REVERT: B  218 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7820 (mm)
REVERT: B  241 VAL cc_start: 0.9419 (OUTLIER) cc_final: 0.9186 (p)
REVERT: B  323 MET cc_start: 0.8736 (ppp) cc_final: 0.7542 (ppp)
REVERT: B  505 SER cc_start: 0.9655 (OUTLIER) cc_final: 0.9417 (p)
REVERT: B  531 LEU cc_start: 0.9544 (tp) cc_final: 0.9295 (tp)
  outliers start: 36
  outliers final: 20
  residues processed: 130
  average time/residue: 0.1407
  time to fit residues: 27.6478
Evaluate side-chains
  113 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue    2 ASN
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  378 LEU
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  447 ILE
Chi-restraints excluded: chain B residue  505 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 105 optimal weight:    0.9980
   chunk 101 optimal weight:   10.0000
   chunk 77 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 75 optimal weight:    7.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
B   2 ASN
B   6 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.054980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.040272 restraints weight = 40290.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.041700 restraints weight = 22759.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.042752 restraints weight = 15480.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8218  Z= 0.166
  Angle     :  0.644  12.007  11162  Z= 0.301
  Chirality :  0.042   0.159   1386
  Planarity :  0.003   0.032   1382
  Dihedral  :  4.180  44.132   1136
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 29.12 %
    Favored  : 66.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.26), residues: 1082
  helix:  1.78 (0.20), residues: 732
  sheet: -1.87 (0.59), residues: 62
  loop : -1.59 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 367 
 HIS   0.003   0.000   HIS B 150 
 PHE   0.016   0.001   PHE B 516 
 TYR   0.009   0.001   TYR A 163 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
REVERT: A   70 MET cc_start: 0.9567 (tpp) cc_final: 0.9169 (mpp)
REVERT: A   80 SER cc_start: 0.9675 (m) cc_final: 0.9250 (t)
REVERT: A  140 GLU cc_start: 0.9137 (tp30) cc_final: 0.8751 (tp30)
REVERT: A  182 MET cc_start: 0.9436 (tpp) cc_final: 0.9119 (tmm)
REVERT: A  218 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7798 (mm)
REVERT: A  269 GLU cc_start: 0.9525 (mp0) cc_final: 0.9172 (mp0)
REVERT: A  323 MET cc_start: 0.8948 (ppp) cc_final: 0.8274 (ppp)
REVERT: A  541 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8961 (mm)
REVERT: B    2 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.8609 (t0)
REVERT: B    6 ASN cc_start: 0.9829 (OUTLIER) cc_final: 0.9478 (m-40)
REVERT: B   48 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9443 (mm)
REVERT: B  131 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: B  140 GLU cc_start: 0.9176 (tp30) cc_final: 0.8873 (tp30)
REVERT: B  182 MET cc_start: 0.9473 (tmm) cc_final: 0.9188 (tmm)
REVERT: B  218 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7929 (mm)
REVERT: B  269 GLU cc_start: 0.9523 (mp0) cc_final: 0.9052 (pm20)
REVERT: B  323 MET cc_start: 0.8682 (ppp) cc_final: 0.7481 (ppp)
REVERT: B  339 LEU cc_start: 0.9729 (mt) cc_final: 0.9195 (pt)
REVERT: B  531 LEU cc_start: 0.9521 (tp) cc_final: 0.9250 (tp)
  outliers start: 37
  outliers final: 19
  residues processed: 129
  average time/residue: 0.1375
  time to fit residues: 27.0388
Evaluate side-chains
  114 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain B residue    2 ASN
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  218 ILE
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  539 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 77 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 75 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   chunk 101 optimal weight:    0.3980
   chunk 65 optimal weight:    5.9990
   overall best weight:    3.0786

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

Flipped N/Q/H residues before XYZ refinement:
A   2 ASN
** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B   6 ASN
B 214 HIS
B 227 GLN
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.052964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.038058 restraints weight = 41364.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.039379 restraints weight = 23633.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.040315 restraints weight = 16180.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8539
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8218  Z= 0.243
  Angle     :  0.665  11.050  11162  Z= 0.325
  Chirality :  0.043   0.162   1386
  Planarity :  0.003   0.029   1382
  Dihedral  :  4.359  49.905   1136
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 29.35 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.26), residues: 1082
  helix:  1.92 (0.20), residues: 732
  sheet: -1.83 (0.61), residues: 62
  loop : -1.48 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 367 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.028   0.002   PHE B 236 
 TYR   0.010   0.001   TYR A 167 
 ARG   0.002   0.000   ARG A 357 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A   70 MET cc_start: 0.9618 (tpp) cc_final: 0.9140 (mpp)
REVERT: A   80 SER cc_start: 0.9693 (m) cc_final: 0.9270 (t)
REVERT: A  140 GLU cc_start: 0.9209 (tp30) cc_final: 0.8843 (tp30)
REVERT: A  182 MET cc_start: 0.9480 (tpp) cc_final: 0.9220 (tmm)
REVERT: A  323 MET cc_start: 0.9104 (ppp) cc_final: 0.8523 (ppp)
REVERT: A  415 MET cc_start: 0.8887 (mpp) cc_final: 0.8085 (mpp)
REVERT: A  420 ASP cc_start: 0.9146 (p0) cc_final: 0.8666 (p0)
REVERT: A  431 LEU cc_start: 0.9489 (tp) cc_final: 0.9274 (mt)
REVERT: A  437 THR cc_start: 0.9682 (OUTLIER) cc_final: 0.9318 (p)
REVERT: B    6 ASN cc_start: 0.9828 (OUTLIER) cc_final: 0.9602 (m110)
REVERT: B  113 MET cc_start: 0.9239 (tmm) cc_final: 0.8996 (ppp)
REVERT: B  131 GLN cc_start: 0.9245 (mm-40) cc_final: 0.8965 (tm-30)
REVERT: B  140 GLU cc_start: 0.9203 (tp30) cc_final: 0.8911 (tp30)
REVERT: B  182 MET cc_start: 0.9544 (tmm) cc_final: 0.9255 (tmm)
REVERT: B  323 MET cc_start: 0.8932 (ppp) cc_final: 0.7977 (ppp)
REVERT: B  339 LEU cc_start: 0.9765 (mt) cc_final: 0.9277 (pt)
REVERT: B  531 LEU cc_start: 0.9556 (tp) cc_final: 0.9335 (tp)
  outliers start: 38
  outliers final: 24
  residues processed: 123
  average time/residue: 0.1424
  time to fit residues: 26.6611
Evaluate side-chains
  110 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain B residue    6 ASN
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  447 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 57 optimal weight:    0.0870
   chunk 35 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 23 optimal weight:   20.0000
   chunk 60 optimal weight:    6.9990
   chunk 86 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    3.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 275 GLN ** 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 = 0.3036 r_free = 0.3036 target = 0.052093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.037325 restraints weight = 42261.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.038652 restraints weight = 23883.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.039614 restraints weight = 16292.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8218  Z= 0.250
  Angle     :  0.688  12.012  11162  Z= 0.330
  Chirality :  0.042   0.159   1386
  Planarity :  0.003   0.028   1382
  Dihedral  :  4.537  54.861   1136
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 31.79 %
    Favored  : 64.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.26), residues: 1082
  helix:  1.87 (0.20), residues: 736
  sheet: -1.85 (0.59), residues: 62
  loop : -1.58 (0.31), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 367 
 HIS   0.003   0.001   HIS B 469 
 PHE   0.019   0.002   PHE B 236 
 TYR   0.009   0.001   TYR A 289 
 ARG   0.001   0.000   ARG A 357 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 90
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A   70 MET cc_start: 0.9633 (tpp) cc_final: 0.9145 (mpp)
REVERT: A   80 SER cc_start: 0.9694 (m) cc_final: 0.9281 (t)
REVERT: A  113 MET cc_start: 0.9478 (tmm) cc_final: 0.9004 (ppp)
REVERT: A  140 GLU cc_start: 0.9203 (tp30) cc_final: 0.8825 (tp30)
REVERT: A  182 MET cc_start: 0.9482 (tpp) cc_final: 0.9241 (tmm)
REVERT: A  203 MET cc_start: 0.9495 (mmm) cc_final: 0.9277 (mmm)
REVERT: A  323 MET cc_start: 0.9145 (ppp) cc_final: 0.8611 (ppp)
REVERT: A  415 MET cc_start: 0.8904 (mpp) cc_final: 0.8149 (mpp)
REVERT: A  431 LEU cc_start: 0.9482 (tp) cc_final: 0.9239 (mt)
REVERT: A  437 THR cc_start: 0.9670 (OUTLIER) cc_final: 0.9316 (p)
REVERT: A  480 MET cc_start: 0.9228 (ptm) cc_final: 0.8666 (ppp)
REVERT: B   80 SER cc_start: 0.9626 (m) cc_final: 0.9163 (t)
REVERT: B  131 GLN cc_start: 0.9272 (mm-40) cc_final: 0.8959 (tm-30)
REVERT: B  140 GLU cc_start: 0.9188 (tp30) cc_final: 0.8899 (tp30)
REVERT: B  182 MET cc_start: 0.9552 (tmm) cc_final: 0.9227 (tmm)
REVERT: B  269 GLU cc_start: 0.9517 (mp0) cc_final: 0.9133 (pm20)
REVERT: B  323 MET cc_start: 0.9000 (ppp) cc_final: 0.8186 (ppp)
REVERT: B  339 LEU cc_start: 0.9744 (mt) cc_final: 0.9222 (pt)
REVERT: B  480 MET cc_start: 0.9281 (ptm) cc_final: 0.8942 (ppp)
REVERT: B  531 LEU cc_start: 0.9590 (tp) cc_final: 0.9320 (tp)
  outliers start: 32
  outliers final: 26
  residues processed: 121
  average time/residue: 0.1436
  time to fit residues: 26.2706
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  383 THR
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  362 ILE
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  447 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 24 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 98 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 64 optimal weight:    7.9990
   chunk 47 optimal weight:    0.1980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 469 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.054065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.039298 restraints weight = 41677.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.040687 restraints weight = 23483.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.041696 restraints weight = 15942.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8518
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8218  Z= 0.178
  Angle     :  0.701  11.534  11162  Z= 0.327
  Chirality :  0.043   0.156   1386
  Planarity :  0.003   0.029   1382
  Dihedral  :  4.470  57.111   1136
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 31.67 %
    Favored  : 64.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.26), residues: 1082
  helix:  2.03 (0.20), residues: 732
  sheet: -1.74 (0.59), residues: 62
  loop : -1.42 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 367 
 HIS   0.003   0.000   HIS B 150 
 PHE   0.015   0.001   PHE A 300 
 TYR   0.008   0.001   TYR A 163 
 ARG   0.002   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.956 
Fit side-chains
REVERT: A   70 MET cc_start: 0.9595 (tpp) cc_final: 0.9139 (mpp)
REVERT: A   80 SER cc_start: 0.9657 (m) cc_final: 0.9225 (t)
REVERT: A  113 MET cc_start: 0.9437 (tmm) cc_final: 0.8968 (ppp)
REVERT: A  140 GLU cc_start: 0.9166 (tp30) cc_final: 0.8777 (tp30)
REVERT: A  182 MET cc_start: 0.9459 (tpp) cc_final: 0.9194 (tmm)
REVERT: A  203 MET cc_start: 0.9513 (mmm) cc_final: 0.9267 (mmm)
REVERT: A  323 MET cc_start: 0.9170 (ppp) cc_final: 0.8389 (ppp)
REVERT: A  396 THR cc_start: 0.9537 (OUTLIER) cc_final: 0.9264 (p)
REVERT: A  415 MET cc_start: 0.8871 (mpp) cc_final: 0.8120 (mpp)
REVERT: A  480 MET cc_start: 0.9269 (ptm) cc_final: 0.8851 (ppp)
REVERT: A  497 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9083 (mp)
REVERT: B   80 SER cc_start: 0.9597 (m) cc_final: 0.9139 (t)
REVERT: B  131 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8963 (tm-30)
REVERT: B  140 GLU cc_start: 0.9156 (tp30) cc_final: 0.8852 (tp30)
REVERT: B  182 MET cc_start: 0.9536 (tmm) cc_final: 0.9185 (tmm)
REVERT: B  269 GLU cc_start: 0.9529 (mp0) cc_final: 0.9118 (pm20)
REVERT: B  323 MET cc_start: 0.8910 (ppp) cc_final: 0.8077 (ppp)
REVERT: B  480 MET cc_start: 0.9343 (ptm) cc_final: 0.9052 (ppp)
REVERT: B  531 LEU cc_start: 0.9536 (tp) cc_final: 0.9270 (tp)
  outliers start: 30
  outliers final: 24
  residues processed: 121
  average time/residue: 0.1445
  time to fit residues: 26.7709
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 LEU
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  285 LYS
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  497 LEU
Chi-restraints excluded: chain A residue  539 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  131 GLN
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  295 VAL
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Chi-restraints excluded: chain B residue  447 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0970
   chunk 18 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0070
   chunk 68 optimal weight:    7.9990
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3130 r_free = 0.3130 target = 0.056010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.041187 restraints weight = 41151.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.042651 restraints weight = 23221.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.043747 restraints weight = 15810.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8218  Z= 0.168
  Angle     :  0.706  12.777  11162  Z= 0.322
  Chirality :  0.042   0.149   1386
  Planarity :  0.003   0.030   1382
  Dihedral  :  4.365  58.559   1136
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 32.60 %
    Favored  : 64.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1082
  helix:  2.00 (0.20), residues: 732
  sheet: -1.55 (0.58), residues: 62
  loop : -1.46 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 367 
 HIS   0.003   0.000   HIS B 150 
 PHE   0.015   0.001   PHE A 300 
 TYR   0.009   0.001   TYR A 163 
 ARG   0.003   0.000   ARG B 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   70 MET cc_start: 0.9580 (tpp) cc_final: 0.9123 (mpp)
REVERT: A   80 SER cc_start: 0.9630 (m) cc_final: 0.9181 (t)
REVERT: A  140 GLU cc_start: 0.9143 (tp30) cc_final: 0.8740 (tp30)
REVERT: A  182 MET cc_start: 0.9469 (tpp) cc_final: 0.9179 (tmm)
REVERT: A  186 MET cc_start: 0.9081 (mmm) cc_final: 0.8647 (mmm)
REVERT: A  203 MET cc_start: 0.9502 (mmm) cc_final: 0.9239 (mmm)
REVERT: A  323 MET cc_start: 0.9170 (ppp) cc_final: 0.8525 (ppp)
REVERT: A  480 MET cc_start: 0.9316 (ptm) cc_final: 0.9014 (pmm)
REVERT: B   48 LEU cc_start: 0.9684 (OUTLIER) cc_final: 0.9444 (mm)
REVERT: B   55 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8673 (p90)
REVERT: B   80 SER cc_start: 0.9571 (m) cc_final: 0.9089 (t)
REVERT: B  113 MET cc_start: 0.9220 (tmm) cc_final: 0.8943 (ppp)
REVERT: B  140 GLU cc_start: 0.9140 (tp30) cc_final: 0.8830 (tp30)
REVERT: B  182 MET cc_start: 0.9491 (tmm) cc_final: 0.9133 (tmm)
REVERT: B  269 GLU cc_start: 0.9529 (mp0) cc_final: 0.9120 (pm20)
REVERT: B  323 MET cc_start: 0.8842 (ppp) cc_final: 0.7927 (ppp)
REVERT: B  480 MET cc_start: 0.9380 (ptm) cc_final: 0.9046 (ppp)
  outliers start: 24
  outliers final: 18
  residues processed: 114
  average time/residue: 0.1377
  time to fit residues: 24.2707
Evaluate side-chains
  107 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 95 optimal weight:    6.9990
   chunk 20 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 25 optimal weight:   20.0000
   chunk 43 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.3988

-------------------------------------------------------------------------------
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 = 0.3107 r_free = 0.3107 target = 0.054957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.039981 restraints weight = 41333.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.041420 restraints weight = 23630.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.042355 restraints weight = 16092.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.5006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8218  Z= 0.183
  Angle     :  0.729  18.861  11162  Z= 0.331
  Chirality :  0.042   0.153   1386
  Planarity :  0.003   0.030   1382
  Dihedral  :  4.366  59.785   1136
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 32.48 %
    Favored  : 64.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1082
  helix:  2.02 (0.20), residues: 732
  sheet: -1.55 (0.58), residues: 62
  loop : -1.38 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 367 
 HIS   0.003   0.000   HIS B 150 
 PHE   0.015   0.001   PHE A 300 
 TYR   0.008   0.001   TYR A 408 
 ARG   0.001   0.000   ARG A 409 

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

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

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2164 Ramachandran restraints generated.
    1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.943 
Fit side-chains
REVERT: A   70 MET cc_start: 0.9608 (tpp) cc_final: 0.9106 (mpp)
REVERT: A   80 SER cc_start: 0.9655 (m) cc_final: 0.9211 (t)
REVERT: A  140 GLU cc_start: 0.9162 (tp30) cc_final: 0.8762 (tp30)
REVERT: A  182 MET cc_start: 0.9475 (tpp) cc_final: 0.9186 (tmm)
REVERT: A  203 MET cc_start: 0.9517 (mmm) cc_final: 0.9254 (mmm)
REVERT: A  323 MET cc_start: 0.9185 (ppp) cc_final: 0.8614 (ppp)
REVERT: A  396 THR cc_start: 0.9522 (OUTLIER) cc_final: 0.9243 (p)
REVERT: A  480 MET cc_start: 0.9240 (ptm) cc_final: 0.9011 (pmm)
REVERT: B   55 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8747 (p90)
REVERT: B   80 SER cc_start: 0.9611 (m) cc_final: 0.9124 (t)
REVERT: B  113 MET cc_start: 0.9281 (tmm) cc_final: 0.9030 (ppp)
REVERT: B  140 GLU cc_start: 0.9150 (tp30) cc_final: 0.8844 (tp30)
REVERT: B  182 MET cc_start: 0.9519 (tmm) cc_final: 0.9167 (tmm)
REVERT: B  269 GLU cc_start: 0.9515 (mp0) cc_final: 0.9105 (pm20)
REVERT: B  323 MET cc_start: 0.8872 (ppp) cc_final: 0.7942 (ppp)
REVERT: B  480 MET cc_start: 0.9309 (ptm) cc_final: 0.9024 (ppp)
  outliers start: 23
  outliers final: 18
  residues processed: 110
  average time/residue: 0.1348
  time to fit residues: 23.1293
Evaluate side-chains
  111 residues out of total 868 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   55 PHE
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  168 VAL
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  283 THR
Chi-restraints excluded: chain A residue  295 VAL
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  396 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain B residue   26 LEU
Chi-restraints excluded: chain B residue   48 LEU
Chi-restraints excluded: chain B residue   55 PHE
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  217 THR
Chi-restraints excluded: chain B residue  400 ILE
Chi-restraints excluded: chain B residue  417 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 15 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 47 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.040684 restraints weight = 41364.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.041995 restraints weight = 23703.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.042969 restraints weight = 16307.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8218  Z= 0.225
  Angle     :  0.738  17.176  11162  Z= 0.343
  Chirality :  0.043   0.161   1386
  Planarity :  0.003   0.030   1382
  Dihedral  :  4.432  56.918   1136
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 32.83 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.26), residues: 1082
  helix:  1.98 (0.20), residues: 738
  sheet: -1.56 (0.61), residues: 62
  loop : -1.31 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 367 
 HIS   0.003   0.001   HIS B 150 
 PHE   0.015   0.001   PHE A 300 
 TYR   0.010   0.001   TYR A 167 
 ARG   0.002   0.000   ARG B  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2180.81 seconds
wall clock time: 40 minutes 13.44 seconds (2413.44 seconds total)