Starting phenix.real_space_refine
on Thu Mar 13 18:50:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zo8_14843/03_2025/7zo8_14843.cif"
  }
  resolution = 3.6
  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=   0.120
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      44      5.16       5
     C    5678      2.51       5
     N    1582      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8952
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4437
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 570, 4422
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 11, 'TRANS': 558}
      Conformer: "B"
        Number of residues, atoms: 570, 4422
          Classifications: {'peptide': 570}
          Link IDs: {'PTRANS': 11, 'TRANS': 558}
          bond proxies already assigned to first conformer: 4478
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'PLC': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
  Restraints were copied for chains:
    B
  Time building chain proxies: 11.11, per 1000 atoms: 1.24
  Number of scatterers: 8952
  At special positions: 0
  Unit cell: (74.825, 109.675, 135.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       2     15.00
     O    1646      8.00
     N    1582      7.00
     C    5678      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: 3.23
  Conformation dependent library (CDL) restraints added in 2.7 seconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      71.7% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 17
      removed outlier: 4.002A  pdb=" N   TYR A  13 " --> pdb=" O   ARG A   9 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LEU A  14 " --> pdb=" O   ALA A  10 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU A  17 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 48
      removed outlier: 3.762A  pdb=" N   THR A  21 " --> pdb=" O   GLU A  17 " (cutoff:3.500A)
      Proline residue:  A  39  - end of helix
    Processing helix  chain 'A' and resid 55 through 100
      removed outlier: 3.625A  pdb=" N   MET A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA A  77 " --> pdb=" O   ALA A  73 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP A  81 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 111
      removed outlier: 3.949A  pdb=" N   HIS A 107 " --> pdb=" O   PRO A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 155
      removed outlier: 3.616A  pdb=" N   MET A 134 " --> pdb=" O   TRP A 130 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ARG A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      Proline residue:  A 149  - end of helix
    Processing helix  chain 'A' and resid 155 through 204
      removed outlier: 3.640A  pdb=" N   GLY A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   LYS A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   HIS A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 211
    Processing helix  chain 'A' and resid 213 through 233
    Processing helix  chain 'A' and resid 235 through 267
      removed outlier: 5.257A  pdb=" N   ASN A 246 " --> pdb=" O   ALA A 242 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ARG A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS A 267 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 316
      removed outlier: 3.505A  pdb=" N   PHE A 278 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 280 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ALA A 304 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LYS A 305 " --> pdb=" O   THR A 301 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU A 308 " --> pdb=" O   ALA A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
    Processing helix  chain 'A' and resid 400 through 402
      No H-bonds generated for 'chain 'A' and resid 400 through 402'
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.890A  pdb=" N   HIS A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 431
      removed outlier: 3.688A  pdb=" N   VAL A 431 " --> pdb=" O   ASP A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 448
      removed outlier: 4.253A  pdb=" N   HIS A 442 " --> pdb=" O   HIS A 438 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ALA A 443 " --> pdb=" O   GLU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 456
      removed outlier: 4.379A  pdb=" N   ALA A 456 " --> pdb=" O   ASP A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 463
      removed outlier: 4.150A  pdb=" N   ASP A 462 " --> pdb=" O   GLU A 459 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   THR A 463 " --> pdb=" O   GLY A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 463'
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 473 through 489
    Processing helix  chain 'A' and resid 503 through 518
      removed outlier: 3.877A  pdb=" N   LYS A 509 " --> pdb=" O   GLU A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 570
    Processing helix  chain 'B' and resid 2 through 17
      removed outlier: 4.002A  pdb=" N   TYR B  13 " --> pdb=" O   ARG B   9 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU B  14 " --> pdb=" O   ALA B  10 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU B  17 " --> pdb=" O   TYR B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 48
      removed outlier: 3.761A  pdb=" N   THR B  21 " --> pdb=" O   GLU B  17 " (cutoff:3.500A)
      Proline residue:  B  39  - end of helix
    Processing helix  chain 'B' and resid 55 through 100
      removed outlier: 3.624A  pdb=" N   MET B  61 " --> pdb=" O   SER B  57 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ALA B  77 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ASP B  81 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 111
      removed outlier: 3.950A  pdb=" N   HIS B 107 " --> pdb=" O   PRO B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 155
      removed outlier: 3.616A  pdb=" N   MET B 134 " --> pdb=" O   TRP B 130 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   ARG B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      Proline residue:  B 149  - end of helix
    Processing helix  chain 'B' and resid 155 through 204
      removed outlier: 3.639A  pdb=" N   GLY B 183 " --> pdb=" O   LYS B 179 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   LYS B 189 " --> pdb=" O   ALA B 185 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   HIS B 190 " --> pdb=" O   ALA B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 211
    Processing helix  chain 'B' and resid 213 through 233
    Processing helix  chain 'B' and resid 235 through 267
      removed outlier: 5.257A  pdb=" N   ASN B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ARG B 247 " --> pdb=" O   SER B 243 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS B 267 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 271 through 316
      removed outlier: 3.504A  pdb=" N   PHE B 278 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY B 280 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ALA B 304 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   LYS B 305 " --> pdb=" O   THR B 301 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLU B 308 " --> pdb=" O   ALA B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 383
    Processing helix  chain 'B' and resid 400 through 402
      No H-bonds generated for 'chain 'B' and resid 400 through 402'
    Processing helix  chain 'B' and resid 403 through 410
      removed outlier: 3.889A  pdb=" N   HIS B 409 " --> pdb=" O   ARG B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 431
      removed outlier: 3.689A  pdb=" N   VAL B 431 " --> pdb=" O   ASP B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 448
      removed outlier: 4.252A  pdb=" N   HIS B 442 " --> pdb=" O   HIS B 438 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ALA B 443 " --> pdb=" O   GLU B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 456
      removed outlier: 4.380A  pdb=" N   ALA B 456 " --> pdb=" O   ASP B 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 463
      removed outlier: 4.150A  pdb=" N   ASP B 462 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   THR B 463 " --> pdb=" O   GLY B 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 459 through 463'
    Processing helix  chain 'B' and resid 466 through 470
    Processing helix  chain 'B' and resid 473 through 489
    Processing helix  chain 'B' and resid 503 through 518
      removed outlier: 3.877A  pdb=" N   LYS B 509 " --> pdb=" O   GLU B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 570
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 5.363A  pdb=" N   VAL A 354 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   VAL A 340 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA A 389 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 414
      removed outlier: 7.216A  pdb=" N   VAL A 539 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   SER A 550 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   PHE A 541 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 548 " --> pdb=" O   PHE A 541 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 5.363A  pdb=" N   VAL B 354 " --> pdb=" O   ASN B 339 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   VAL B 340 " --> pdb=" O   ALA B 389 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   ALA B 389 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 411 through 414
      removed outlier: 7.215A  pdb=" N   VAL B 539 " --> pdb=" O   SER B 550 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   SER B 550 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   PHE B 541 " --> pdb=" O   VAL B 548 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   VAL B 548 " --> pdb=" O   PHE B 541 " (cutoff:3.500A)

    641 hydrogen bonds defined for protein.
    1883 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: 2.99

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1470
        1.31 -     1.43: 2282
        1.43 -     1.55: 5262
        1.55 -     1.68: 4
        1.68 -     1.80: 86
  Bond restraints: 9104
  Sorted by residual:
  bond pdb=" CB  PLC A 601 "
       pdb=" O3  PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.414 -0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" CB  PLC B 601 "
       pdb=" O3  PLC B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.414 -0.087 2.00e-02 2.50e+03 1.90e+01
  bond pdb=" C'  PLC A 601 "
       pdb=" O2  PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.416 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C'  PLC B 601 "
       pdb=" O2  PLC B 601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.415 -0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" N   PLC A 601 "
       pdb=" C5  PLC A 601 "
    ideal  model  delta    sigma   weight residual
    1.508  1.450  0.058 2.00e-02 2.50e+03 8.35e+00
  ... (remaining 9099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.73: 12250
        3.73 -     7.47: 60
        7.47 -    11.20: 4
       11.20 -    14.93: 0
       14.93 -    18.66: 4
  Bond angle restraints: 12318
  Sorted by residual:
  angle pdb=" O1P PLC A 601 "
        pdb=" P   PLC A 601 "
        pdb=" O2P PLC A 601 "
      ideal   model   delta    sigma   weight residual
     119.61  100.95   18.66 3.00e+00 1.11e-01 3.87e+01
  angle pdb=" O1P PLC B 601 "
        pdb=" P   PLC B 601 "
        pdb=" O2P PLC B 601 "
      ideal   model   delta    sigma   weight residual
     119.61  101.00   18.61 3.00e+00 1.11e-01 3.85e+01
  angle pdb=" O3P PLC A 601 "
        pdb=" P   PLC A 601 "
        pdb=" O4P PLC A 601 "
      ideal   model   delta    sigma   weight residual
      93.62  110.31  -16.69 3.00e+00 1.11e-01 3.09e+01
  angle pdb=" O3P PLC B 601 "
        pdb=" P   PLC B 601 "
        pdb=" O4P PLC B 601 "
      ideal   model   delta    sigma   weight residual
      93.62  110.28  -16.66 3.00e+00 1.11e-01 3.09e+01
  angle pdb=" C   ARG A 135 "
        pdb=" N   GLN A 136 "
        pdb=" CA  GLN A 136 "
      ideal   model   delta    sigma   weight residual
     120.58  114.67    5.91 1.71e+00 3.42e-01 1.20e+01
  ... (remaining 12313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.06: 5159
       27.06 -    54.11: 283
       54.11 -    81.17: 36
       81.17 -   108.23: 6
      108.23 -   135.28: 6
  Dihedral angle restraints: 5490
    sinusoidal: 2184
      harmonic: 3306
  Sorted by residual:
  dihedral pdb=" CA  SER A  50 "
           pdb=" C   SER A  50 "
           pdb=" N   ASP A  51 "
           pdb=" CA  ASP A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.41   24.59     0      5.00e+00 4.00e-02 2.42e+01
  dihedral pdb=" CA  SER B  50 "
           pdb=" C   SER B  50 "
           pdb=" N   ASP B  51 "
           pdb=" CA  ASP B  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.46   24.54     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" C3  PLC B 601 "
           pdb=" C1  PLC B 601 "
           pdb=" C2  PLC B 601 "
           pdb=" O3P PLC B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      67.16 -157.56 -135.28     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 5487 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 968
       0.035 -    0.069: 349
       0.069 -    0.104: 79
       0.104 -    0.139: 34
       0.139 -    0.174: 10
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  PRO A 103 "
            pdb=" N   PRO A 103 "
            pdb=" C   PRO A 103 "
            pdb=" CB  PRO A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  PRO B 103 "
            pdb=" N   PRO B 103 "
            pdb=" C   PRO B 103 "
            pdb=" CB  PRO B 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.21e-01
  chirality pdb=" CA  HIS B 137 "
            pdb=" N   HIS B 137 "
            pdb=" C   HIS B 137 "
            pdb=" CB  HIS B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.61e-01
  ... (remaining 1437 not shown)

  Planarity restraints: 1572
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 134 "    0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   MET B 134 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   MET B 134 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ARG B 135 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 134 "   -0.018 2.00e-02 2.50e+03   3.53e-02 1.25e+01
        pdb=" C   MET A 134 "    0.061 2.00e-02 2.50e+03
        pdb=" O   MET A 134 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ARG A 135 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 359 "    0.038 5.00e-02 4.00e+02   5.74e-02 5.26e+00
        pdb=" N   PRO B 360 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 360 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 360 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1569 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1892
        2.79 -     3.31: 9249
        3.31 -     3.84: 14444
        3.84 -     4.37: 15461
        4.37 -     4.90: 28189
  Nonbonded interactions: 69235
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 490 "
            pdb=" O   ILE A 492 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OG  SER B 490 "
            pdb=" O   ILE B 492 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   GLY B 561 "
            pdb=" OG  SER B 564 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   GLY A 561 "
            pdb=" OG  SER A 564 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NH2 ARG A 423 "
            pdb=" OE2 GLU B 217 "
     model   vdw
     2.346 3.120
  ... (remaining 69230 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: 0.09
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=0.50 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:             171.080
  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:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.080
  Process input model:                     32.630
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  207.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
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      :  0.004   0.087   9104  Z= 0.273
  Angle     :  0.704  18.665  12318  Z= 0.336
  Chirality :  0.041   0.174   1440
  Planarity :  0.004   0.057   1572
  Dihedral  : 16.849 135.282   3350
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.75 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  0.21 %
    Favored  : 99.36 %
  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:  1.72 (0.26), residues: 1140
  helix:  2.12 (0.19), residues: 782
  sheet:  0.61 (0.58), residues: 70
  loop : -1.58 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 137 
 PHE   0.018   0.001   PHE A 195 
 TYR   0.007   0.001   TYR A 461 
 ARG   0.007   0.000   ARG B 383 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.984 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1642
  time to fit residues: 27.8318
Evaluate side-chains
  90 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    5.9990
   chunk 86 optimal weight:    0.5980
   chunk 47 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 54 optimal weight:   30.0000
   chunk 66 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 204 ASN
B 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.204485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.153885 restraints weight = 28802.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.149255 restraints weight = 32669.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.143900 restraints weight = 19254.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3478
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3478 r_free = 0.3478    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.0921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9104  Z= 0.322
  Angle     :  0.624   8.378  12318  Z= 0.328
  Chirality :  0.043   0.182   1440
  Planarity :  0.004   0.040   1572
  Dihedral  : 12.409 130.321   1320
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.49 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  7.22 %
    Favored  : 91.83 %
  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:  1.51 (0.26), residues: 1140
  helix:  1.94 (0.19), residues: 788
  sheet:  0.76 (0.57), residues: 70
  loop : -1.71 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 238 
 HIS   0.007   0.001   HIS A 137 
 PHE   0.017   0.001   PHE A 195 
 TYR   0.023   0.001   TYR A 263 
 ARG   0.003   0.000   ARG A 383 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.914 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 100
  average time/residue: 0.1943
  time to fit residues: 29.7180
Evaluate side-chains
  98 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue  422 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 104 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 38 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 50 optimal weight:   30.0000
   chunk 63 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0670
   overall best weight:    1.5722

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.203417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.151299 restraints weight = 24433.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.147594 restraints weight = 31316.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.142629 restraints weight = 19018.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3473 r_free = 0.3473    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.1208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9104  Z= 0.311
  Angle     :  0.618   9.344  12318  Z= 0.321
  Chirality :  0.043   0.176   1440
  Planarity :  0.004   0.037   1572
  Dihedral  : 11.525 112.925   1320
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.75 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.66 %
    Favored  : 89.38 %
  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:  1.46 (0.26), residues: 1140
  helix:  1.92 (0.19), residues: 782
  sheet:  0.71 (0.56), residues: 70
  loop : -1.73 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 238 
 HIS   0.007   0.001   HIS A 137 
 PHE   0.017   0.001   PHE B 195 
 TYR   0.023   0.001   TYR A 263 
 ARG   0.004   0.000   ARG B 423 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.914 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 94
  average time/residue: 0.1614
  time to fit residues: 23.3885
Evaluate side-chains
  96 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  414 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 99 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 112 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A  47 GLN
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 GLN
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.205837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.153430 restraints weight = 23206.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.148443 restraints weight = 29155.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.141126 restraints weight = 20300.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3451
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3451 r_free = 0.3451    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3451
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.1261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9104  Z= 0.206
  Angle     :  0.561  10.010  12318  Z= 0.289
  Chirality :  0.041   0.174   1440
  Planarity :  0.004   0.036   1572
  Dihedral  : 10.392  91.503   1320
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.14 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 10.40 %
    Favored  : 88.32 %
  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:  1.65 (0.26), residues: 1140
  helix:  2.09 (0.19), residues: 782
  sheet:  0.70 (0.56), residues: 70
  loop : -1.72 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 238 
 HIS   0.005   0.001   HIS A 137 
 PHE   0.017   0.001   PHE A 195 
 TYR   0.023   0.001   TYR A 263 
 ARG   0.002   0.000   ARG B 271 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.936 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 100
  average time/residue: 0.1682
  time to fit residues: 26.4463
Evaluate side-chains
  96 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  414 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 86 optimal weight:    0.6980
   chunk 104 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.202284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.150124 restraints weight = 22083.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.146103 restraints weight = 30055.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.140003 restraints weight = 19160.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3471
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3471 r_free = 0.3471    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3471
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9104  Z= 0.237
  Angle     :  0.568   9.030  12318  Z= 0.294
  Chirality :  0.041   0.173   1440
  Planarity :  0.004   0.036   1572
  Dihedral  :  9.747  77.068   1320
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.40 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.89 %
    Favored  : 86.73 %
  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:  1.60 (0.26), residues: 1140
  helix:  2.07 (0.19), residues: 780
  sheet:  0.79 (0.58), residues: 70
  loop : -1.80 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 238 
 HIS   0.005   0.001   HIS B 137 
 PHE   0.016   0.001   PHE B 195 
 TYR   0.024   0.001   TYR B 263 
 ARG   0.002   0.000   ARG A 288 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 1.526 
Fit side-chains
  outliers start: 9
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1967
  time to fit residues: 29.1623
Evaluate side-chains
  97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue    4 LEU
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  414 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 111 optimal weight:   20.0000
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 105 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.206983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.152743 restraints weight = 20963.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.153114 restraints weight = 22158.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.151853 restraints weight = 13185.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3340
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3340 r_free = 0.3340    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3340
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9104  Z= 0.423
  Angle     :  0.671   9.010  12318  Z= 0.348
  Chirality :  0.045   0.200   1440
  Planarity :  0.004   0.052   1572
  Dihedral  :  9.779  80.637   1320
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.31 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.31 %
    Favored  : 86.09 %
  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:  1.27 (0.25), residues: 1140
  helix:  1.79 (0.19), residues: 780
  sheet:  0.74 (0.58), residues: 70
  loop : -1.84 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 106 
 HIS   0.008   0.001   HIS B 137 
 PHE   0.018   0.002   PHE B 278 
 TYR   0.027   0.002   TYR A 263 
 ARG   0.004   0.000   ARG B 271 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 1.108 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1858
  time to fit residues: 28.3589
Evaluate side-chains
  97 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  414 VAL
Chi-restraints excluded: chain B residue  453 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:   20.0000
   chunk 50 optimal weight:   30.0000
   chunk 17 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0270
   chunk 34 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.206214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.154156 restraints weight = 27841.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.151410 restraints weight = 33659.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.148395 restraints weight = 18545.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3522
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3522 r_free = 0.3522    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3522
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9104  Z= 0.208
  Angle     :  0.569   8.473  12318  Z= 0.290
  Chirality :  0.040   0.173   1440
  Planarity :  0.004   0.037   1572
  Dihedral  :  9.110  64.980   1320
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.49 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.06 %
    Favored  : 85.99 %
  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:  1.64 (0.26), residues: 1140
  helix:  2.09 (0.19), residues: 780
  sheet:  0.87 (0.59), residues: 70
  loop : -1.77 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 106 
 HIS   0.004   0.001   HIS B 137 
 PHE   0.017   0.001   PHE B 195 
 TYR   0.023   0.001   TYR B 263 
 ARG   0.002   0.000   ARG A 247 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 2.340 
Fit side-chains
REVERT: B  108 GLN cc_start: 0.8388 (mp10) cc_final: 0.7715 (mp10)
  outliers start: 5
  outliers final: 4
  residues processed: 94
  average time/residue: 0.1724
  time to fit residues: 27.0550
Evaluate side-chains
  92 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 1.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 54 optimal weight:   20.0000
   chunk 100 optimal weight:    6.9990
   chunk 97 optimal weight:    5.9990
   chunk 72 optimal weight:    0.7980
   chunk 104 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.202428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.147295 restraints weight = 25116.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.144192 restraints weight = 31975.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.138167 restraints weight = 14158.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3400
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3400 r_free = 0.3400    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3400
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1767

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9104  Z= 0.357
  Angle     :  0.644  10.676  12318  Z= 0.328
  Chirality :  0.043   0.179   1440
  Planarity :  0.004   0.043   1572
  Dihedral  :  9.222  71.421   1320
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.14 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 13.16 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.46 (0.26), residues: 1140
  helix:  1.93 (0.19), residues: 780
  sheet:  0.87 (0.59), residues: 70
  loop : -1.79 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP B 106 
 HIS   0.007   0.001   HIS B 137 
 PHE   0.021   0.002   PHE B 195 
 TYR   0.024   0.001   TYR A 263 
 ARG   0.003   0.000   ARG B 135 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 1.620 
Fit side-chains
  outliers start: 6
  outliers final: 5
  residues processed: 91
  average time/residue: 0.1669
  time to fit residues: 24.5362
Evaluate side-chains
  94 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 89
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 36 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 102 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 101 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.206665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.158076 restraints weight = 18366.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.152908 restraints weight = 27706.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.153226 restraints weight = 9092.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9104  Z= 0.202
  Angle     :  0.577  11.010  12318  Z= 0.291
  Chirality :  0.040   0.171   1440
  Planarity :  0.004   0.037   1572
  Dihedral  :  8.925  60.429   1320
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.58 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.27 %
    Favored  : 85.46 %
  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:  1.72 (0.26), residues: 1140
  helix:  2.15 (0.19), residues: 780
  sheet:  0.88 (0.59), residues: 70
  loop : -1.74 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 106 
 HIS   0.004   0.001   HIS B 191 
 PHE   0.016   0.001   PHE A 195 
 TYR   0.022   0.001   TYR B 263 
 ARG   0.001   0.000   ARG B 433 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  248 MET cc_start: 0.8386 (mmm) cc_final: 0.7858 (mmm)
REVERT: B  108 GLN cc_start: 0.8455 (mp10) cc_final: 0.7739 (mp10)
REVERT: B  248 MET cc_start: 0.8306 (mmm) cc_final: 0.7815 (mmm)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.1645
  time to fit residues: 24.7088
Evaluate side-chains
  100 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 44 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 89 optimal weight:   20.0000
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.206990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.154538 restraints weight = 23483.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.151352 restraints weight = 30352.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.148343 restraints weight = 15509.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9104  Z= 0.218
  Angle     :  0.587  10.904  12318  Z= 0.294
  Chirality :  0.040   0.168   1440
  Planarity :  0.004   0.038   1572
  Dihedral  :  8.806  59.301   1320
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.23 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.59 %
    Favored  : 85.46 %
  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:  1.77 (0.26), residues: 1140
  helix:  2.20 (0.19), residues: 780
  sheet:  0.86 (0.59), residues: 70
  loop : -1.73 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 191 
 PHE   0.017   0.001   PHE B 195 
 TYR   0.023   0.001   TYR A 263 
 ARG   0.002   0.000   ARG A 433 

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 GLN cc_start: 0.8408 (mp10) cc_final: 0.7750 (mp10)
REVERT: B  108 GLN cc_start: 0.8406 (mp10) cc_final: 0.7770 (mp10)
  outliers start: 5
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1910
  time to fit residues: 29.5523
Evaluate side-chains
  101 residues out of total 934 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 LEU
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  425 VAL
Chi-restraints excluded: chain B residue   16 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 101 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 41 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.207174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.157014 restraints weight = 10598.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.156445 restraints weight = 21499.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.157811 restraints weight = 16264.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9104  Z= 0.212
  Angle     :  0.581  10.954  12318  Z= 0.291
  Chirality :  0.040   0.165   1440
  Planarity :  0.004   0.039   1572
  Dihedral  :  8.675  56.314   1320
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  4.40 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.69 %
    Favored  : 85.35 %
  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:  1.82 (0.26), residues: 1140
  helix:  2.21 (0.19), residues: 782
  sheet:  0.94 (0.60), residues: 70
  loop : -1.67 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 106 
 HIS   0.005   0.001   HIS B 191 
 PHE   0.017   0.001   PHE B 195 
 TYR   0.023   0.001   TYR B 263 
 ARG   0.004   0.000   ARG B 433 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3558.00 seconds
wall clock time: 65 minutes 12.51 seconds (3912.51 seconds total)