Starting phenix.real_space_refine
on Sat Jul 26 16:38:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jdj_61393/07_2025/9jdj_61393_neut.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.042
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      64      5.16       5
     C    5728      2.51       5
     N    1244      2.21       5
     O    1420      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8456
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 4142
          Classifications: {'peptide': 524}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 27, 'TRANS': 496}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 20
    Chain: "B"
      Number of atoms: 4142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 524, 4142
          Classifications: {'peptide': 524}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 27, 'TRANS': 496}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 36
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 32
          Planarities with less than four sites: {'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 20
    Chain: "A"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 86
          Unusual residues: {'CLR': 2, 'D10': 1, 'D12': 1, 'OCT': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 86
          Unusual residues: {'CLR': 2, 'D10': 1, 'D12': 1, 'OCT': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.74, per 1000 atoms: 0.80
  Number of scatterers: 8456
  At special positions: 0
  Unit cell: (104.445, 104.445, 106.555, 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      64     16.00
     O    1420      8.00
     N    1244      7.00
     C    5728      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 171 " distance=2.03

  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: 2.84
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 2 sheets defined
      79.3% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 65
      removed outlier: 3.654A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 79 through 90
    Processing helix  chain 'A' and resid 90 through 106
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.663A  pdb=" N   TRP A 113 " --> pdb=" O   GLY A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 152
      removed outlier: 4.079A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   TYR A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   VAL A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 180
      removed outlier: 4.144A  pdb=" N   LYS A 178 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   ASN A 179 " --> pdb=" O   THR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 217 through 237
    Processing helix  chain 'A' and resid 245 through 267
      removed outlier: 4.092A  pdb=" N   THR A 249 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.599A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 287
      removed outlier: 3.678A  pdb=" N   LEU A 285 " --> pdb=" O   ASP A 281 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU A 286 " --> pdb=" O   ILE A 282 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ASP A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 281 through 287'
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.490A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 316
      removed outlier: 3.630A  pdb=" N   TYR A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ASN A 316 " --> pdb=" O   LEU A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 356
      removed outlier: 3.770A  pdb=" N   ASP A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ALA A 343 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 363
      removed outlier: 4.417A  pdb=" N   ALA A 363 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 4.034A  pdb=" N   SER A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLU A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP A 416 " --> pdb=" O   THR A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 444
    Processing helix  chain 'A' and resid 445 through 449
      removed outlier: 5.696A  pdb=" N   GLU A 449 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 3.772A  pdb=" N   VAL A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 481
      removed outlier: 3.697A  pdb=" N   LEU A 469 " --> pdb=" O   GLY A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 3.735A  pdb=" N   GLY A 491 " --> pdb=" O   ASN A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 510
    Processing helix  chain 'A' and resid 510 through 526
    Processing helix  chain 'A' and resid 539 through 555
    Processing helix  chain 'A' and resid 555 through 568
    Processing helix  chain 'A' and resid 571 through 581
    Processing helix  chain 'B' and resid 60 through 65
      removed outlier: 3.542A  pdb=" N   VAL B  64 " --> pdb=" O   GLY B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 74
    Processing helix  chain 'B' and resid 76 through 78
      No H-bonds generated for 'chain 'B' and resid 76 through 78'
    Processing helix  chain 'B' and resid 79 through 90
    Processing helix  chain 'B' and resid 90 through 106
    Processing helix  chain 'B' and resid 108 through 117
      removed outlier: 3.663A  pdb=" N   TRP B 113 " --> pdb=" O   GLY B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 152
      removed outlier: 4.080A  pdb=" N   TYR B 125 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   TYR B 137 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   VAL B 140 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU B 142 " --> pdb=" O   TYR B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 180
      removed outlier: 4.157A  pdb=" N   LYS B 178 " --> pdb=" O   ASP B 174 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ASN B 179 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 201
    Processing helix  chain 'B' and resid 217 through 237
    Processing helix  chain 'B' and resid 245 through 267
      removed outlier: 4.091A  pdb=" N   THR B 249 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 269 through 279
      removed outlier: 3.599A  pdb=" N   GLY B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 287
      removed outlier: 3.678A  pdb=" N   LEU B 285 " --> pdb=" O   ASP B 281 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU B 286 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASP B 287 " --> pdb=" O   THR B 283 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 281 through 287'
    Processing helix  chain 'B' and resid 287 through 302
      removed outlier: 4.489A  pdb=" N   TRP B 291 " --> pdb=" O   ASP B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 316
      removed outlier: 3.630A  pdb=" N   TYR B 315 " --> pdb=" O   SER B 311 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ASN B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 356
      removed outlier: 3.771A  pdb=" N   ASP B 325 " --> pdb=" O   ASN B 321 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA B 343 " --> pdb=" O   VAL B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 363
      removed outlier: 4.417A  pdb=" N   ALA B 363 " --> pdb=" O   ILE B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 379
    Processing helix  chain 'B' and resid 383 through 418
      removed outlier: 4.034A  pdb=" N   SER B 402 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU B 408 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLN B 410 " --> pdb=" O   GLU B 406 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ILE B 411 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ASP B 416 " --> pdb=" O   THR B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 444
    Processing helix  chain 'B' and resid 445 through 449
      removed outlier: 5.695A  pdb=" N   GLU B 449 " --> pdb=" O   MET B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.771A  pdb=" N   VAL B 454 " --> pdb=" O   GLY B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 481
      removed outlier: 3.697A  pdb=" N   LEU B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 496
      removed outlier: 3.734A  pdb=" N   GLY B 491 " --> pdb=" O   ASN B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 510
    Processing helix  chain 'B' and resid 510 through 526
    Processing helix  chain 'B' and resid 539 through 555
    Processing helix  chain 'B' and resid 555 through 568
    Processing helix  chain 'B' and resid 571 through 581
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532
    Processing sheet with id=AA2, first strand: chain 'B' and resid 531 through 532

    545 hydrogen bonds defined for protein.
    1623 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: 2.49

  Time building geometry restraints manager: 2.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2395
        1.34 -     1.46: 2020
        1.46 -     1.58: 4229
        1.58 -     1.69: 0
        1.69 -     1.81: 92
  Bond restraints: 8736
  Sorted by residual:
  bond pdb=" N   PHE A  67 "
       pdb=" CA  PHE A  67 "
    ideal  model  delta    sigma   weight residual
    1.462  1.490 -0.028 7.70e-03 1.69e+04 1.31e+01
  bond pdb=" N   VAL A  64 "
       pdb=" CA  VAL A  64 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.09e-02 8.42e+03 1.02e+01
  bond pdb=" N   PHE B  67 "
       pdb=" CA  PHE B  67 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.20e-03 1.18e+04 1.02e+01
  bond pdb=" N   VAL B  64 "
       pdb=" CA  VAL B  64 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.22e-02 6.72e+03 9.46e+00
  bond pdb=" N   VAL B 227 "
       pdb=" CA  VAL B 227 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.036 1.19e-02 7.06e+03 9.26e+00
  ... (remaining 8731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 11097
        1.93 -     3.86: 788
        3.86 -     5.79: 37
        5.79 -     7.72: 4
        7.72 -     9.65: 2
  Bond angle restraints: 11928
  Sorted by residual:
  angle pdb=" N   THR B 379 "
        pdb=" CA  THR B 379 "
        pdb=" C   THR B 379 "
      ideal   model   delta    sigma   weight residual
     113.01  107.94    5.07 1.20e+00 6.94e-01 1.78e+01
  angle pdb=" CA  ASN A  74 "
        pdb=" C   ASN A  74 "
        pdb=" O   ASN A  74 "
      ideal   model   delta    sigma   weight residual
     122.63  118.03    4.60 1.29e+00 6.01e-01 1.27e+01
  angle pdb=" CA  THR B 568 "
        pdb=" CB  THR B 568 "
        pdb=" OG1 THR B 568 "
      ideal   model   delta    sigma   weight residual
     109.60  104.29    5.31 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" CA  THR A 568 "
        pdb=" CB  THR A 568 "
        pdb=" OG1 THR A 568 "
      ideal   model   delta    sigma   weight residual
     109.60  104.29    5.31 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" N   SER B 121 "
        pdb=" CA  SER B 121 "
        pdb=" C   SER B 121 "
      ideal   model   delta    sigma   weight residual
     113.16  108.94    4.22 1.24e+00 6.50e-01 1.16e+01
  ... (remaining 11923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 4686
       17.48 -    34.96: 329
       34.96 -    52.43: 74
       52.43 -    69.91: 25
       69.91 -    87.39: 4
  Dihedral angle restraints: 5118
    sinusoidal: 2100
      harmonic: 3018
  Sorted by residual:
  dihedral pdb=" CD  ARG B  66 "
           pdb=" NE  ARG B  66 "
           pdb=" CZ  ARG B  66 "
           pdb=" NH1 ARG B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -41.42   41.42     1      1.00e+01 1.00e-02 2.40e+01
  dihedral pdb=" CD  ARG A 564 "
           pdb=" NE  ARG A 564 "
           pdb=" CZ  ARG A 564 "
           pdb=" NH1 ARG A 564 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -38.42   38.42     1      1.00e+01 1.00e-02 2.08e+01
  dihedral pdb=" CD  ARG B 177 "
           pdb=" NE  ARG B 177 "
           pdb=" CZ  ARG B 177 "
           pdb=" NH1 ARG B 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -32.40   32.40     1      1.00e+01 1.00e-02 1.49e+01
  ... (remaining 5115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 834
       0.045 -    0.090: 280
       0.090 -    0.135: 151
       0.135 -    0.180: 38
       0.180 -    0.225: 23
  Chirality restraints: 1326
  Sorted by residual:
  chirality pdb=" CA  ILE A 196 "
            pdb=" N   ILE A 196 "
            pdb=" C   ILE A 196 "
            pdb=" CB  ILE A 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  ILE B 196 "
            pdb=" N   ILE B 196 "
            pdb=" C   ILE B 196 "
            pdb=" CB  ILE B 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" CA  ILE B 141 "
            pdb=" N   ILE B 141 "
            pdb=" C   ILE B 141 "
            pdb=" CB  ILE B 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1323 not shown)

  Planarity restraints: 1428
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  66 "    0.714 9.50e-02 1.11e+02   3.20e-01 6.26e+01
        pdb=" NE  ARG B  66 "   -0.044 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  66 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  66 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  66 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 564 "    0.665 9.50e-02 1.11e+02   2.98e-01 5.43e+01
        pdb=" NE  ARG A 564 "   -0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 564 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 564 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 564 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 177 "    0.569 9.50e-02 1.11e+02   2.55e-01 3.99e+01
        pdb=" NE  ARG B 177 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 177 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 177 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 177 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1425 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 613
        2.74 -     3.28: 9509
        3.28 -     3.82: 14407
        3.82 -     4.36: 18361
        4.36 -     4.90: 29601
  Nonbonded interactions: 72491
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A  66 "
            pdb=" OD2 ASP A 459 "
     model   vdw
     2.200 3.120
  nonbonded pdb=" O   LEU A 549 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   LEU B 549 "
            pdb=" OG  SER B 552 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   PHE A 342 "
            pdb=" OG  SER A 346 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   PHE B 342 "
            pdb=" OG  SER B 346 "
     model   vdw
     2.278 3.040
  ... (remaining 72486 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' and (resid 57 through 587 or resid 705))
  selection = (chain 'B' and (resid 57 through 587 or resid 705))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  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:         0.100
  Set scattering table:                    0.090
  Process input model:                     25.380
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.030
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6802
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      :  0.007   0.051   8738  Z= 0.537
  Angle     :  0.898   9.652  11932  Z= 0.668
  Chirality :  0.063   0.225   1326
  Planarity :  0.016   0.320   1428
  Dihedral  : 13.188  87.391   3204
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 10.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  1.58 %
    Favored  : 97.29 %
  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:  0.01 (0.24), residues: 1040
  helix:  0.60 (0.18), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.23 (0.32), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 387 
 HIS   0.001   0.001   HIS A 212 
 PHE   0.024   0.002   PHE A 421 
 TYR   0.015   0.001   TYR B  69 
 ARG   0.004   0.001   ARG A 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.23009 (  545)
  hydrogen bonds       : angle       7.53309 ( 1623)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.72478 (    4)
  covalent geometry    : bond        0.00734 ( 8736)
  covalent geometry    : angle       0.89782 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 304
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.8300 (mt) cc_final: 0.7758 (tp)
REVERT: A  392 PHE cc_start: 0.7414 (m-10) cc_final: 0.7115 (m-80)
REVERT: A  408 GLU cc_start: 0.7804 (pt0) cc_final: 0.7433 (tm-30)
REVERT: A  490 ASP cc_start: 0.7001 (m-30) cc_final: 0.6361 (t0)
REVERT: A  521 ILE cc_start: 0.8997 (mm) cc_final: 0.8785 (mt)
REVERT: A  579 LEU cc_start: 0.5989 (mt) cc_final: 0.5555 (mt)
REVERT: B   98 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6881 (mm-30)
REVERT: B  118 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8116 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8469 (mt) cc_final: 0.7843 (tp)
REVERT: B  176 MET cc_start: 0.6649 (tpt) cc_final: 0.6327 (tpp)
REVERT: B  326 CYS cc_start: 0.7672 (t) cc_final: 0.7131 (m)
REVERT: B  429 GLU cc_start: 0.7876 (pt0) cc_final: 0.7407 (pt0)
REVERT: B  470 TRP cc_start: 0.7811 (t-100) cc_final: 0.7554 (t-100)
REVERT: B  473 PHE cc_start: 0.7033 (t80) cc_final: 0.6827 (t80)
REVERT: B  490 ASP cc_start: 0.7076 (m-30) cc_final: 0.6538 (t0)
REVERT: B  579 LEU cc_start: 0.6262 (mt) cc_final: 0.5678 (mt)
  outliers start: 10
  outliers final: 3
  residues processed: 308
  average time/residue: 0.1964
  time to fit residues: 83.7243
Evaluate side-chains
  184 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 181
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  383 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 60 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 HIS
** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 164 HIS
** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 353 GLN
B 410 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.178917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.150653 restraints weight = 11012.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.154189 restraints weight = 6818.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156559 restraints weight = 5110.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7384
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8738  Z= 0.160
  Angle     :  0.604   8.848  11932  Z= 0.316
  Chirality :  0.042   0.158   1326
  Planarity :  0.006   0.055   1428
  Dihedral  :  6.238  59.763   1440
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 11.88 %
    Favored  : 85.63 %
  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 (0.25), residues: 1040
  helix:  1.27 (0.18), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.09 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 547 
 HIS   0.003   0.001   HIS B 212 
 PHE   0.023   0.002   PHE A 391 
 TYR   0.024   0.002   TYR B 418 
 ARG   0.005   0.001   ARG A 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05382 (  545)
  hydrogen bonds       : angle       4.96828 ( 1623)
  SS BOND              : bond        0.00812 (    2)
  SS BOND              : angle       1.80608 (    4)
  covalent geometry    : bond        0.00344 ( 8736)
  covalent geometry    : angle       0.60306 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 202
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ARG cc_start: 0.7628 (tmm-80) cc_final: 0.7302 (ttp-110)
REVERT: A  490 ASP cc_start: 0.6612 (m-30) cc_final: 0.6387 (t0)
REVERT: B  118 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8234 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8367 (mt) cc_final: 0.8041 (tp)
REVERT: B  428 ARG cc_start: 0.7733 (tmm-80) cc_final: 0.7493 (ttp-110)
  outliers start: 22
  outliers final: 12
  residues processed: 211
  average time/residue: 0.1885
  time to fit residues: 55.9514
Evaluate side-chains
  178 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 166
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 13 optimal weight:    0.4980
   chunk 69 optimal weight:    1.9990
   chunk 60 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0970
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 103 GLN
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 316 ASN
B 103 GLN
B 316 ASN
B 321 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.168471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141214 restraints weight = 11519.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144287 restraints weight = 7372.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.146282 restraints weight = 5630.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8738  Z= 0.134
  Angle     :  0.558   9.436  11932  Z= 0.286
  Chirality :  0.040   0.171   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.087  57.117   1438
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 13.24 %
    Favored  : 83.94 %
  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:  0.99 (0.25), residues: 1040
  helix:  1.36 (0.18), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.10 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 470 
 HIS   0.004   0.001   HIS A 170 
 PHE   0.016   0.002   PHE B 191 
 TYR   0.018   0.001   TYR B 418 
 ARG   0.002   0.000   ARG B 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04645 (  545)
  hydrogen bonds       : angle       4.52091 ( 1623)
  SS BOND              : bond        0.00338 (    2)
  SS BOND              : angle       1.33218 (    4)
  covalent geometry    : bond        0.00293 ( 8736)
  covalent geometry    : angle       0.55766 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 191
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  490 ASP cc_start: 0.6642 (m-30) cc_final: 0.6404 (t0)
REVERT: B  118 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8249 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8416 (mt) cc_final: 0.8148 (tp)
  outliers start: 25
  outliers final: 10
  residues processed: 203
  average time/residue: 0.1819
  time to fit residues: 51.9730
Evaluate side-chains
  183 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 173
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue  100 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  466 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 103 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.161649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.133163 restraints weight = 11552.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.136086 restraints weight = 7562.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.138049 restraints weight = 5863.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8738  Z= 0.179
  Angle     :  0.598   8.531  11932  Z= 0.306
  Chirality :  0.042   0.159   1326
  Planarity :  0.005   0.053   1428
  Dihedral  :  6.274  48.641   1436
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 14.71 %
    Favored  : 82.47 %
  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:  0.87 (0.25), residues: 1040
  helix:  1.28 (0.18), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.20 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 470 
 HIS   0.005   0.001   HIS A 170 
 PHE   0.016   0.002   PHE A  67 
 TYR   0.017   0.002   TYR A 461 
 ARG   0.006   0.001   ARG B 428 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04676 (  545)
  hydrogen bonds       : angle       4.52941 ( 1623)
  SS BOND              : bond        0.00430 (    2)
  SS BOND              : angle       1.11558 (    4)
  covalent geometry    : bond        0.00427 ( 8736)
  covalent geometry    : angle       0.59777 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 TYR cc_start: 0.8550 (t80) cc_final: 0.7902 (t80)
REVERT: A  428 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7468 (ttp-110)
REVERT: A  490 ASP cc_start: 0.6914 (m-30) cc_final: 0.6640 (t0)
REVERT: B  118 PRO cc_start: 0.8585 (Cg_exo) cc_final: 0.8135 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8579 (mt) cc_final: 0.8313 (tp)
REVERT: B  428 ARG cc_start: 0.7889 (ttp-110) cc_final: 0.7565 (ttp-110)
REVERT: B  561 ILE cc_start: 0.8942 (mt) cc_final: 0.8680 (mm)
  outliers start: 25
  outliers final: 17
  residues processed: 182
  average time/residue: 0.1950
  time to fit residues: 49.5996
Evaluate side-chains
  178 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  119 LEU
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 0 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 297 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 = 0.3896 r_free = 0.3896 target = 0.165131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137011 restraints weight = 11369.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.140009 restraints weight = 7432.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141901 restraints weight = 5757.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8738  Z= 0.140
  Angle     :  0.560   8.886  11932  Z= 0.285
  Chirality :  0.040   0.159   1326
  Planarity :  0.005   0.046   1428
  Dihedral  :  6.104  48.690   1436
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.74 %
    Favored  : 81.33 %
  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:  1.03 (0.25), residues: 1040
  helix:  1.38 (0.18), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.08 (0.32), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 218 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.018   0.002   PHE A  67 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.005   0.001   ARG B 284 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04303 (  545)
  hydrogen bonds       : angle       4.38297 ( 1623)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       1.05688 (    4)
  covalent geometry    : bond        0.00327 ( 8736)
  covalent geometry    : angle       0.55988 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 PHE cc_start: 0.8560 (m-10) cc_final: 0.8357 (m-80)
REVERT: A  428 ARG cc_start: 0.7871 (ttp-110) cc_final: 0.7389 (ttp-110)
REVERT: A  490 ASP cc_start: 0.6886 (m-30) cc_final: 0.6637 (t0)
REVERT: B  279 TYR cc_start: 0.6620 (m-10) cc_final: 0.6278 (m-10)
REVERT: B  561 ILE cc_start: 0.8904 (mt) cc_final: 0.8618 (mm)
REVERT: B  564 ARG cc_start: 0.7698 (mmm-85) cc_final: 0.7002 (mtp180)
  outliers start: 17
  outliers final: 12
  residues processed: 182
  average time/residue: 0.2089
  time to fit residues: 53.3302
Evaluate side-chains
  171 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 26 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.164869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.136945 restraints weight = 11298.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.139956 restraints weight = 7368.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.141771 restraints weight = 5680.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8738  Z= 0.126
  Angle     :  0.549   8.726  11932  Z= 0.278
  Chirality :  0.040   0.160   1326
  Planarity :  0.005   0.044   1428
  Dihedral  :  6.027  49.627   1436
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.99 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.19 (0.25), residues: 1040
  helix:  1.46 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.93 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 470 
 HIS   0.003   0.001   HIS A 170 
 PHE   0.014   0.001   PHE B  67 
 TYR   0.011   0.001   TYR A  69 
 ARG   0.005   0.000   ARG B 428 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 (  545)
  hydrogen bonds       : angle       4.33095 ( 1623)
  SS BOND              : bond        0.00303 (    2)
  SS BOND              : angle       0.96526 (    4)
  covalent geometry    : bond        0.00288 ( 8736)
  covalent geometry    : angle       0.54897 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 173
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6559 (m-10) cc_final: 0.6158 (m-10)
REVERT: A  297 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8420 (tp40)
REVERT: A  428 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7362 (ttp-110)
REVERT: A  490 ASP cc_start: 0.6881 (m-30) cc_final: 0.6641 (t0)
REVERT: B  279 TYR cc_start: 0.6605 (m-10) cc_final: 0.6231 (m-10)
REVERT: B  428 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7684 (ttp-110)
  outliers start: 14
  outliers final: 8
  residues processed: 182
  average time/residue: 0.2001
  time to fit residues: 51.3728
Evaluate side-chains
  173 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 164
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  297 GLN
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0670
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 101 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 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 = 0.3888 r_free = 0.3888 target = 0.164523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.136322 restraints weight = 11462.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.139323 restraints weight = 7476.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.141295 restraints weight = 5769.788|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.4595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8738  Z= 0.128
  Angle     :  0.567   8.547  11932  Z= 0.286
  Chirality :  0.040   0.160   1326
  Planarity :  0.005   0.046   1428
  Dihedral  :  6.031  50.074   1436
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 17.76 %
    Favored  : 79.86 %
  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:  1.23 (0.25), residues: 1040
  helix:  1.49 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.91 (0.33), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 470 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.022   0.001   PHE A  67 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.006   0.001   ARG B 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  545)
  hydrogen bonds       : angle       4.35325 ( 1623)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       1.51200 (    4)
  covalent geometry    : bond        0.00293 ( 8736)
  covalent geometry    : angle       0.56617 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6611 (m-10) cc_final: 0.6211 (m-10)
REVERT: A  428 ARG cc_start: 0.7914 (ttp-110) cc_final: 0.7416 (ttp-110)
REVERT: B  279 TYR cc_start: 0.6631 (m-10) cc_final: 0.6239 (m-10)
REVERT: B  428 ARG cc_start: 0.7856 (ttp-110) cc_final: 0.7590 (ttp-110)
  outliers start: 21
  outliers final: 14
  residues processed: 184
  average time/residue: 0.1900
  time to fit residues: 49.1011
Evaluate side-chains
  175 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 161
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9990
   chunk 99 optimal weight:    0.7980
   chunk 68 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 94 optimal weight:    6.9990
   chunk 26 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 297 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 = 0.3894 r_free = 0.3894 target = 0.164785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136503 restraints weight = 11509.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.139474 restraints weight = 7548.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141438 restraints weight = 5838.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8738  Z= 0.141
  Angle     :  0.592   8.218  11932  Z= 0.299
  Chirality :  0.042   0.317   1326
  Planarity :  0.005   0.048   1428
  Dihedral  :  6.137  51.490   1436
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.23 %
    Favored  : 78.73 %
  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:  1.21 (0.25), residues: 1040
  helix:  1.49 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.92 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 470 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.020   0.002   PHE A  67 
 TYR   0.014   0.001   TYR B 323 
 ARG   0.006   0.001   ARG B 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  545)
  hydrogen bonds       : angle       4.37481 ( 1623)
  SS BOND              : bond        0.00325 (    2)
  SS BOND              : angle       1.21455 (    4)
  covalent geometry    : bond        0.00332 ( 8736)
  covalent geometry    : angle       0.59211 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 166
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6746 (m-10) cc_final: 0.6356 (m-10)
REVERT: A  428 ARG cc_start: 0.7930 (ttp-110) cc_final: 0.7422 (ttp-110)
REVERT: B  279 TYR cc_start: 0.6663 (m-10) cc_final: 0.6300 (m-10)
  outliers start: 18
  outliers final: 16
  residues processed: 178
  average time/residue: 0.1919
  time to fit residues: 47.8832
Evaluate side-chains
  179 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 163
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  486 ASP
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 52 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 10 optimal weight:    0.4980
   chunk 77 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 297 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.167006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138635 restraints weight = 11452.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.141589 restraints weight = 7493.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.143570 restraints weight = 5831.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8738  Z= 0.125
  Angle     :  0.590   8.714  11932  Z= 0.298
  Chirality :  0.041   0.335   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.064  52.875   1436
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 19.80 %
    Favored  : 78.51 %
  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: 1040
  helix:  1.54 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.90 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 470 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.022   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 323 
 ARG   0.009   0.001   ARG B 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03961 (  545)
  hydrogen bonds       : angle       4.33175 ( 1623)
  SS BOND              : bond        0.00274 (    2)
  SS BOND              : angle       1.12508 (    4)
  covalent geometry    : bond        0.00287 ( 8736)
  covalent geometry    : angle       0.58937 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6669 (m-10) cc_final: 0.6358 (m-10)
REVERT: A  297 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8384 (tp40)
REVERT: A  428 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7392 (ttp-110)
REVERT: A  522 PHE cc_start: 0.7286 (m-80) cc_final: 0.6937 (m-80)
REVERT: B  279 TYR cc_start: 0.6693 (m-10) cc_final: 0.6318 (m-10)
REVERT: B  428 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7665 (ttp-110)
  outliers start: 15
  outliers final: 13
  residues processed: 182
  average time/residue: 0.1961
  time to fit residues: 49.8271
Evaluate side-chains
  177 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  297 GLN
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0870
   chunk 5 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 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 = 0.3914 r_free = 0.3914 target = 0.166530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.138291 restraints weight = 11373.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.141303 restraints weight = 7464.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143234 restraints weight = 5778.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8738  Z= 0.130
  Angle     :  0.598   9.643  11932  Z= 0.302
  Chirality :  0.041   0.305   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.087  53.360   1436
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 19.80 %
    Favored  : 78.39 %
  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: 1040
  helix:  1.51 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.88 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 470 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.029   0.001   PHE A  67 
 TYR   0.016   0.001   TYR B 323 
 ARG   0.006   0.000   ARG B 428 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03968 (  545)
  hydrogen bonds       : angle       4.37364 ( 1623)
  SS BOND              : bond        0.00262 (    2)
  SS BOND              : angle       1.06522 (    4)
  covalent geometry    : bond        0.00304 ( 8736)
  covalent geometry    : angle       0.59767 (11928)

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

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

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2080 Ramachandran restraints generated.
    1040 Oldfield, 0 Emsley, 1040 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6720 (m-10) cc_final: 0.6409 (m-10)
REVERT: A  428 ARG cc_start: 0.7899 (ttp-110) cc_final: 0.7393 (ttp-110)
REVERT: A  522 PHE cc_start: 0.7266 (m-80) cc_final: 0.6949 (m-80)
REVERT: B  279 TYR cc_start: 0.6706 (m-10) cc_final: 0.6336 (m-10)
REVERT: B  428 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7644 (ttp-110)
  outliers start: 16
  outliers final: 15
  residues processed: 171
  average time/residue: 0.1956
  time to fit residues: 46.6552
Evaluate side-chains
  171 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 156
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  298 ILE
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  326 CYS
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  215 SER
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0570
   chunk 2 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 297 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 = 0.3925 r_free = 0.3925 target = 0.167726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139200 restraints weight = 11559.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.142198 restraints weight = 7562.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.144182 restraints weight = 5859.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   8738  Z= 0.125
  Angle     :  0.593   9.536  11932  Z= 0.302
  Chirality :  0.041   0.314   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.071  56.093   1436
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 20.14 %
    Favored  : 78.51 %
  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:  1.29 (0.26), residues: 1040
  helix:  1.55 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.90 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 470 
 HIS   0.002   0.001   HIS A 170 
 PHE   0.022   0.001   PHE A  67 
 TYR   0.015   0.001   TYR B 323 
 ARG   0.008   0.001   ARG B 564 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  545)
  hydrogen bonds       : angle       4.36282 ( 1623)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       0.98688 (    4)
  covalent geometry    : bond        0.00288 ( 8736)
  covalent geometry    : angle       0.59246 (11928)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2975.16 seconds
wall clock time: 52 minutes 11.78 seconds (3131.78 seconds total)