Starting phenix.real_space_refine
on Wed Sep 17 12:41:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jdj_61393/09_2025/9jdj_61393_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jdj_61393/09_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_61393/09_2025/9jdj_61393.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jdj_61393/09_2025/9jdj_61393.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jdj_61393/09_2025/9jdj_61393_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jdj_61393/09_2025/9jdj_61393_neut.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.14, per 1000 atoms: 0.25
  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: 0.90
  Conformation dependent library (CDL) restraints added in 322.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.22
  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: 1.32

  Time building geometry restraints manager: 1.14 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: 0.02
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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.200
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.670
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (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
 ARG   0.004   0.001   ARG A 564 
 TYR   0.015   0.001   TYR B  69 
 PHE   0.024   0.002   PHE A 421 
 TRP   0.011   0.002   TRP A 387 
 HIS   0.001   0.001   HIS A 212 

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

*********************** 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  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 LEU cc_start: 0.8300 (mt) cc_final: 0.7678 (tt)
REVERT: A  392 PHE cc_start: 0.7414 (m-10) cc_final: 0.7110 (m-80)
REVERT: A  408 GLU cc_start: 0.7804 (pt0) cc_final: 0.7432 (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: 0.5513 (mt)
REVERT: B   98 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6880 (mm-30)
REVERT: B  118 PRO cc_start: 0.8361 (Cg_exo) cc_final: 0.8127 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8469 (mt) cc_final: 0.7836 (tt)
REVERT: B  176 MET cc_start: 0.6649 (tpt) cc_final: 0.6328 (tpp)
REVERT: B  326 CYS cc_start: 0.7672 (t) cc_final: 0.7133 (m)
REVERT: B  429 GLU cc_start: 0.7876 (pt0) cc_final: 0.7409 (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: 0.6825 (t80)
REVERT: B  490 ASP cc_start: 0.7076 (m-30) cc_final: 0.6537 (t0)
REVERT: B  555 LEU cc_start: 0.8703 (tp) cc_final: 0.8501 (tp)
REVERT: B  579 LEU cc_start: 0.6262 (mt) cc_final: 0.5670 (mt)
  outliers start: 10
  outliers final: 3
  residues processed: 308
  average time/residue: 0.0920
  time to fit residues: 39.7249
Evaluate side-chains
  183 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 180
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0570
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.163154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.135021 restraints weight = 11533.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.137643 restraints weight = 7990.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.139385 restraints weight = 6382.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140303 restraints weight = 5539.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.140898 restraints weight = 5106.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8738  Z= 0.156
  Angle     :  0.608   9.027  11932  Z= 0.316
  Chirality :  0.042   0.160   1326
  Planarity :  0.006   0.054   1428
  Dihedral  :  6.225  59.661   1440
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.99 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.25), residues: 1040
  helix:  1.26 (0.18), residues: 740
  sheet:  None (None), residues: 0
  loop : -1.08 (0.32), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 177 
 TYR   0.024   0.002   TYR B 418 
 PHE   0.023   0.002   PHE A 391 
 TRP   0.012   0.001   TRP A 547 
 HIS   0.002   0.001   HIS B 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 8736)
  covalent geometry    : angle       0.60726 (11928)
  SS BOND              : bond        0.00264 (    2)
  SS BOND              : angle       1.75288 (    4)
  hydrogen bonds       : bond        0.05218 (  545)
  hydrogen bonds       : angle       4.91216 ( 1623)

*********************** 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
  227 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 203
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: A  428 ARG cc_start: 0.7631 (tmm-80) cc_final: 0.7309 (ttp-110)
REVERT: A  579 LEU cc_start: 0.5692 (mt) cc_final: 0.5455 (mt)
REVERT: B  118 PRO cc_start: 0.8534 (Cg_exo) cc_final: 0.8229 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8343 (mt) cc_final: 0.8024 (tp)
REVERT: B  428 ARG cc_start: 0.7695 (tmm-80) cc_final: 0.7453 (ttp-110)
  outliers start: 24
  outliers final: 10
  residues processed: 211
  average time/residue: 0.0868
  time to fit residues: 26.1508
Evaluate side-chains
  176 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
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  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 90 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 33 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.167740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.140416 restraints weight = 11361.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.143491 restraints weight = 7301.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.145385 restraints weight = 5590.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.146753 restraints weight = 4756.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.147346 restraints weight = 4278.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8738  Z= 0.139
  Angle     :  0.568   9.464  11932  Z= 0.291
  Chirality :  0.041   0.163   1326
  Planarity :  0.005   0.052   1428
  Dihedral  :  6.046  55.790   1436
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 13.12 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1040
  helix:  1.32 (0.18), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.13 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 284 
 TYR   0.018   0.002   TYR B 418 
 PHE   0.021   0.002   PHE A 421 
 TRP   0.008   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8736)
  covalent geometry    : angle       0.56760 (11928)
  SS BOND              : bond        0.00372 (    2)
  SS BOND              : angle       1.23807 (    4)
  hydrogen bonds       : bond        0.04667 (  545)
  hydrogen bonds       : angle       4.52711 ( 1623)

*********************** 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
  206 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 183
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 PHE cc_start: 0.8696 (m-10) cc_final: 0.8408 (m-80)
REVERT: B  118 PRO cc_start: 0.8493 (Cg_exo) cc_final: 0.8215 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8417 (mt) cc_final: 0.8149 (tp)
  outliers start: 23
  outliers final: 10
  residues processed: 194
  average time/residue: 0.0885
  time to fit residues: 24.3849
Evaluate side-chains
  173 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 163
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
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  357 VAL
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue  314 SER
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  495 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 90 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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 = 0.3910 r_free = 0.3910 target = 0.166039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.138176 restraints weight = 11652.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.141211 restraints weight = 7516.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.143208 restraints weight = 5759.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.144431 restraints weight = 4897.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.144943 restraints weight = 4418.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7464
moved from start:          0.4102

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= 0.146
  Angle     :  0.572   8.867  11932  Z= 0.292
  Chirality :  0.041   0.154   1326
  Planarity :  0.005   0.050   1428
  Dihedral  :  6.051  51.600   1436
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.93 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.25), residues: 1040
  helix:  1.38 (0.18), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.13 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 428 
 TYR   0.015   0.001   TYR B 418 
 PHE   0.016   0.002   PHE A  67 
 TRP   0.011   0.001   TRP A 144 
 HIS   0.004   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8736)
  covalent geometry    : angle       0.57144 (11928)
  SS BOND              : bond        0.00371 (    2)
  SS BOND              : angle       1.03392 (    4)
  hydrogen bonds       : bond        0.04365 (  545)
  hydrogen bonds       : angle       4.41585 ( 1623)

*********************** 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
  199 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 PHE cc_start: 0.8735 (m-10) cc_final: 0.8533 (m-80)
REVERT: A  428 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7485 (ttp-110)
REVERT: B  118 PRO cc_start: 0.8546 (Cg_exo) cc_final: 0.8118 (Cg_endo)
REVERT: B  119 LEU cc_start: 0.8514 (mt) cc_final: 0.8281 (tp)
REVERT: B  428 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7558 (ttp-110)
REVERT: B  561 ILE cc_start: 0.8944 (mt) cc_final: 0.8737 (mm)
  outliers start: 23
  outliers final: 17
  residues processed: 185
  average time/residue: 0.0840
  time to fit residues: 21.9421
Evaluate side-chains
  181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  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   64 VAL
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  111 THR
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  383 LEU
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  495 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 75 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.165836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.138032 restraints weight = 11476.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.141111 restraints weight = 7409.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143101 restraints weight = 5670.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.144103 restraints weight = 4814.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.145029 restraints weight = 4397.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4342

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= 0.139
  Angle     :  0.559   8.875  11932  Z= 0.285
  Chirality :  0.040   0.159   1326
  Planarity :  0.005   0.046   1428
  Dihedral  :  6.052  50.022   1436
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.74 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1040
  helix:  1.46 (0.18), residues: 744
  sheet:  None (None), residues: 0
  loop : -1.00 (0.32), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 284 
 TYR   0.012   0.001   TYR B 453 
 PHE   0.018   0.002   PHE A  67 
 TRP   0.010   0.001   TRP B 470 
 HIS   0.003   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8736)
  covalent geometry    : angle       0.55883 (11928)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       0.99547 (    4)
  hydrogen bonds       : bond        0.04180 (  545)
  hydrogen bonds       : angle       4.34735 ( 1623)

*********************** 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
  191 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  297 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8440 (tp40)
REVERT: A  392 PHE cc_start: 0.8701 (m-10) cc_final: 0.8497 (m-80)
REVERT: A  428 ARG cc_start: 0.7891 (ttp-110) cc_final: 0.7435 (ttp-110)
REVERT: B  176 MET cc_start: 0.6825 (mmm) cc_final: 0.6410 (mmm)
REVERT: B  279 TYR cc_start: 0.6598 (m-10) cc_final: 0.6246 (m-10)
REVERT: B  561 ILE cc_start: 0.8896 (mt) cc_final: 0.8633 (mm)
REVERT: B  564 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.6995 (mtp180)
  outliers start: 19
  outliers final: 13
  residues processed: 182
  average time/residue: 0.0862
  time to fit residues: 22.1548
Evaluate side-chains
  180 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
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 A residue  555 LEU
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  383 LEU
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  495 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    6.9990
   chunk 36 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3858 r_free = 0.3858 target = 0.161581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133165 restraints weight = 11527.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.136035 restraints weight = 7579.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137919 restraints weight = 5877.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138886 restraints weight = 5041.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.139623 restraints weight = 4611.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8738  Z= 0.187
  Angle     :  0.597   8.217  11932  Z= 0.304
  Chirality :  0.042   0.165   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.336  49.069   1436
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 16.29 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.25), residues: 1040
  helix:  1.34 (0.19), residues: 746
  sheet:  None (None), residues: 0
  loop : -1.01 (0.33), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 428 
 TYR   0.016   0.002   TYR A  69 
 PHE   0.016   0.002   PHE B  79 
 TRP   0.012   0.001   TRP B 470 
 HIS   0.003   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 8736)
  covalent geometry    : angle       0.59632 (11928)
  SS BOND              : bond        0.00396 (    2)
  SS BOND              : angle       1.04739 (    4)
  hydrogen bonds       : bond        0.04464 (  545)
  hydrogen bonds       : angle       4.50745 ( 1623)

*********************** 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
  197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  428 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7444 (ttp-110)
REVERT: B  176 MET cc_start: 0.6905 (mmm) cc_final: 0.6481 (mmm)
REVERT: B  279 TYR cc_start: 0.6689 (m-10) cc_final: 0.6324 (m-10)
REVERT: B  428 ARG cc_start: 0.7952 (ttp-110) cc_final: 0.7703 (ttp-110)
REVERT: B  561 ILE cc_start: 0.9008 (mt) cc_final: 0.8774 (mm)
  outliers start: 28
  outliers final: 22
  residues processed: 185
  average time/residue: 0.0865
  time to fit residues: 22.7060
Evaluate side-chains
  182 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  207 SER
Chi-restraints excluded: chain A residue  210 ILE
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 A residue  555 LEU
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  326 CYS
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  466 VAL
Chi-restraints excluded: chain B residue  478 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0050
   chunk 47 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 78 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.7396

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.164772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.136565 restraints weight = 11537.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139554 restraints weight = 7472.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.141531 restraints weight = 5753.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.142646 restraints weight = 4903.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.143429 restraints weight = 4456.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.4659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8738  Z= 0.135
  Angle     :  0.571   8.538  11932  Z= 0.290
  Chirality :  0.040   0.162   1326
  Planarity :  0.005   0.046   1428
  Dihedral  :  6.183  52.059   1436
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.53 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1040
  helix:  1.45 (0.19), residues: 742
  sheet:  None (None), residues: 0
  loop : -0.95 (0.33), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 564 
 TYR   0.012   0.001   TYR A  69 
 PHE   0.013   0.001   PHE B  79 
 TRP   0.012   0.001   TRP A 113 
 HIS   0.002   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8736)
  covalent geometry    : angle       0.57130 (11928)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.97018 (    4)
  hydrogen bonds       : bond        0.04099 (  545)
  hydrogen bonds       : angle       4.38125 ( 1623)

*********************** 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
  197 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6725 (m-10) cc_final: 0.6336 (m-10)
REVERT: A  392 PHE cc_start: 0.8494 (m-10) cc_final: 0.8274 (m-80)
REVERT: A  428 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7457 (ttp-110)
REVERT: B  176 MET cc_start: 0.6798 (mmm) cc_final: 0.6334 (mmm)
REVERT: B  279 TYR cc_start: 0.6603 (m-10) cc_final: 0.6265 (m-10)
REVERT: B  428 ARG cc_start: 0.7836 (ttp-110) cc_final: 0.7576 (ttp-110)
REVERT: B  561 ILE cc_start: 0.9038 (mt) cc_final: 0.8805 (mm)
  outliers start: 22
  outliers final: 15
  residues processed: 186
  average time/residue: 0.0883
  time to fit residues: 22.9948
Evaluate side-chains
  176 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 161
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  207 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 A residue  555 LEU
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  326 CYS
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
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:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.3884 r_free = 0.3884 target = 0.163873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.135557 restraints weight = 11475.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.138546 restraints weight = 7534.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140481 restraints weight = 5830.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.141618 restraints weight = 4973.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.142440 restraints weight = 4524.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   8738  Z= 0.144
  Angle     :  0.587   8.410  11932  Z= 0.297
  Chirality :  0.042   0.335   1326
  Planarity :  0.005   0.048   1428
  Dihedral  :  6.241  53.788   1436
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 18.33 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.25), residues: 1040
  helix:  1.46 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.87 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 564 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.020   0.002   PHE A  67 
 TRP   0.010   0.001   TRP B 218 
 HIS   0.003   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 8736)
  covalent geometry    : angle       0.58635 (11928)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.33434 (    4)
  hydrogen bonds       : bond        0.04107 (  545)
  hydrogen bonds       : angle       4.38256 ( 1623)

*********************** 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
  181 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6730 (m-10) cc_final: 0.6339 (m-10)
REVERT: A  392 PHE cc_start: 0.8571 (m-10) cc_final: 0.8356 (m-80)
REVERT: A  428 ARG cc_start: 0.7904 (ttp-110) cc_final: 0.7422 (ttp-110)
REVERT: B  176 MET cc_start: 0.6720 (mmm) cc_final: 0.6281 (mmm)
REVERT: B  279 TYR cc_start: 0.6626 (m-10) cc_final: 0.6285 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 171
  average time/residue: 0.0926
  time to fit residues: 22.0687
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
Chi-restraints excluded: chain A residue  207 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  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
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  298 ILE
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
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 19 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    9.9990
   chunk 79 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0370
   chunk 87 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.165587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.137655 restraints weight = 11321.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.140649 restraints weight = 7347.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142625 restraints weight = 5651.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143737 restraints weight = 4812.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144538 restraints weight = 4376.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
moved from start:          0.4872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8738  Z= 0.130
  Angle     :  0.584   8.913  11932  Z= 0.296
  Chirality :  0.041   0.285   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.218  57.381   1436
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 19.00 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.23 (0.25), residues: 1040
  helix:  1.49 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.86 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 564 
 TYR   0.014   0.001   TYR B 323 
 PHE   0.022   0.001   PHE A  67 
 TRP   0.009   0.001   TRP B 218 
 HIS   0.002   0.001   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8736)
  covalent geometry    : angle       0.58362 (11928)
  SS BOND              : bond        0.00341 (    2)
  SS BOND              : angle       1.23215 (    4)
  hydrogen bonds       : bond        0.03984 (  545)
  hydrogen bonds       : angle       4.36765 ( 1623)

*********************** 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
  174 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 159
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6763 (m-10) cc_final: 0.6402 (m-10)
REVERT: A  428 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7448 (ttp-110)
REVERT: B  176 MET cc_start: 0.6675 (mmm) cc_final: 0.6283 (mmm)
REVERT: B  279 TYR cc_start: 0.6680 (m-10) cc_final: 0.6336 (m-10)
REVERT: B  428 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7672 (ttp-110)
  outliers start: 15
  outliers final: 14
  residues processed: 165
  average time/residue: 0.0895
  time to fit residues: 20.7296
Evaluate side-chains
  168 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
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  357 VAL
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  359 ILE
Chi-restraints excluded: chain B residue  383 LEU
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 60 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 95 optimal weight:    0.0470
   chunk 59 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
A 103 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 = 0.166987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138979 restraints weight = 11270.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.141962 restraints weight = 7339.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143909 restraints weight = 5665.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.145123 restraints weight = 4822.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.145730 restraints weight = 4367.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.5017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   8738  Z= 0.123
  Angle     :  0.577   8.880  11932  Z= 0.294
  Chirality :  0.041   0.256   1326
  Planarity :  0.005   0.049   1428
  Dihedral  :  6.009  55.898   1436
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 19.68 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.26), residues: 1040
  helix:  1.55 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.83 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 428 
 TYR   0.014   0.001   TYR B 323 
 PHE   0.023   0.001   PHE A  67 
 TRP   0.008   0.001   TRP B 218 
 HIS   0.002   0.000   HIS A 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8736)
  covalent geometry    : angle       0.57670 (11928)
  SS BOND              : bond        0.00247 (    2)
  SS BOND              : angle       1.16962 (    4)
  hydrogen bonds       : bond        0.03879 (  545)
  hydrogen bonds       : angle       4.33650 ( 1623)

********************** 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
  177 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 165
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 TYR cc_start: 0.6770 (m-10) cc_final: 0.6428 (m-10)
REVERT: A  428 ARG cc_start: 0.7931 (ttp-110) cc_final: 0.7455 (ttp-110)
REVERT: B  279 TYR cc_start: 0.6638 (m-10) cc_final: 0.6317 (m-10)
REVERT: B  428 ARG cc_start: 0.7918 (ttp-110) cc_final: 0.7652 (ttp-110)
  outliers start: 12
  outliers final: 12
  residues processed: 173
  average time/residue: 0.0909
  time to fit residues: 22.2912
Evaluate side-chains
  164 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  111 THR
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  528 VAL
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain B residue  326 CYS
Chi-restraints excluded: chain B residue  383 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0070
   chunk 37 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.167053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.138901 restraints weight = 11256.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.141920 restraints weight = 7332.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143890 restraints weight = 5661.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.144907 restraints weight = 4828.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.145797 restraints weight = 4413.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8738  Z= 0.126
  Angle     :  0.594   9.034  11932  Z= 0.299
  Chirality :  0.041   0.253   1326
  Planarity :  0.005   0.050   1428
  Dihedral  :  5.861  56.237   1436
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.91 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.25), residues: 1040
  helix:  1.54 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.82 (0.33), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 428 
 TYR   0.015   0.001   TYR B 323 
 PHE   0.022   0.001   PHE A  96 
 TRP   0.010   0.001   TRP B 144 
 HIS   0.002   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8736)
  covalent geometry    : angle       0.59402 (11928)
  SS BOND              : bond        0.00278 (    2)
  SS BOND              : angle       0.97843 (    4)
  hydrogen bonds       : bond        0.03911 (  545)
  hydrogen bonds       : angle       4.36148 ( 1623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.30 seconds
wall clock time: 27 minutes 35.15 seconds (1655.15 seconds total)