Starting phenix.real_space_refine
on Wed Jul 30 07:40:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dlu_7957/07_2025/6dlu_7957_neut.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.001 sd=   0.006
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      66      5.16       5
     C    7512      2.51       5
     N    2105      2.21       5
     O    2300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11991
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 5918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 734, 5918
          Classifications: {'peptide': 734}
          Link IDs: {'CIS': 13, 'PTRANS': 26, 'TRANS': 694}
          Chain breaks: 1
    Chain: "P"
      Number of atoms: 6007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 6007
          Classifications: {'peptide': 747}
          Link IDs: {'CIS': 12, 'PTRANS': 26, 'TRANS': 708}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GCP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "P"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GCP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 10.94, per 1000 atoms: 0.91
  Number of scatterers: 11991
  At special positions: 0
  Unit cell: (216.14, 199.02, 112.35, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      66     16.00
     P       6     15.00
     Mg      2     11.99
     O    2300      8.00
     N    2105      7.00
     C    7512      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.68
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2804

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 5 sheets defined
      52.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 19
    Processing helix  chain 'B' and resid 43 through 53
    Processing helix  chain 'B' and resid 93 through 110
      removed outlier: 3.662A  pdb=" N   VAL B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 165
      removed outlier: 3.992A  pdb=" N   PHE B 163 " --> pdb=" O   MET B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 185 through 194
    Processing helix  chain 'B' and resid 216 through 221
    Processing helix  chain 'B' and resid 238 through 244
    Processing helix  chain 'B' and resid 247 through 262
    Processing helix  chain 'B' and resid 273 through 290
      removed outlier: 3.511A  pdb=" N   LEU B 277 " --> pdb=" O   GLY B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 309
      removed outlier: 3.710A  pdb=" N   LEU B 300 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   SER B 306 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ILE B 307 " --> pdb=" O   GLN B 303 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   LYS B 309 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 315
      removed outlier: 3.820A  pdb=" N   TYR B 314 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 321 through 345
    Processing helix  chain 'B' and resid 360 through 368
      removed outlier: 3.873A  pdb=" N   PHE B 366 " --> pdb=" O   ILE B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 376
    Processing helix  chain 'B' and resid 381 through 395
      removed outlier: 3.969A  pdb=" N   ARG B 385 " --> pdb=" O   GLU B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 417
    Processing helix  chain 'B' and resid 420 through 442
      removed outlier: 3.509A  pdb=" N   CYS B 424 " --> pdb=" O   ILE B 420 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   SER B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   THR B 438 " --> pdb=" O   GLU B 434 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ARG B 440 " --> pdb=" O   ILE B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 482
      removed outlier: 3.894A  pdb=" N   GLY B 469 " --> pdb=" O   ARG B 465 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ARG B 470 " --> pdb=" O   GLU B 466 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLU B 482 " --> pdb=" O   LEU B 478 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 507
    Processing helix  chain 'B' and resid 609 through 624
      removed outlier: 3.959A  pdb=" N   VAL B 613 " --> pdb=" O   THR B 609 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP B 614 " --> pdb=" O   GLN B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 636
      removed outlier: 3.516A  pdb=" N   GLU B 634 " --> pdb=" O   GLY B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 689
      Proline residue:  B 682  - end of helix
      removed outlier: 3.714A  pdb=" N   LEU B 688 " --> pdb=" O   THR B 684 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 700
    Processing helix  chain 'B' and resid 700 through 706
    Processing helix  chain 'B' and resid 718 through 748
    Processing helix  chain 'P' and resid 4 through 23
      Proline residue:  P  11  - end of helix
    Processing helix  chain 'P' and resid 43 through 53
      removed outlier: 3.733A  pdb=" N   VAL P  47 " --> pdb=" O   GLY P  43 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 93 through 109
    Processing helix  chain 'P' and resid 151 through 165
      removed outlier: 4.194A  pdb=" N   PHE P 163 " --> pdb=" O   MET P 159 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 180 through 183
    Processing helix  chain 'P' and resid 184 through 194
    Processing helix  chain 'P' and resid 206 through 210
      removed outlier: 3.509A  pdb=" N   LEU P 209 " --> pdb=" O   LYS P 206 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET P 210 " --> pdb=" O   LEU P 207 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 206 through 210'
    Processing helix  chain 'P' and resid 216 through 221
    Processing helix  chain 'P' and resid 238 through 244
    Processing helix  chain 'P' and resid 247 through 262
    Processing helix  chain 'P' and resid 273 through 312
      Proline residue:  P 294  - end of helix
      removed outlier: 3.798A  pdb=" N   SER P 306 " --> pdb=" O   SER P 302 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE P 307 " --> pdb=" O   GLN P 303 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   LYS P 309 " --> pdb=" O   LEU P 305 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   GLU P 310 " --> pdb=" O   SER P 306 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 313 through 315
      No H-bonds generated for 'chain 'P' and resid 313 through 315'
    Processing helix  chain 'P' and resid 321 through 344
      removed outlier: 3.646A  pdb=" N   LYS P 325 " --> pdb=" O   ASP P 321 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 359 through 367
    Processing helix  chain 'P' and resid 371 through 376
      removed outlier: 3.994A  pdb=" N   VAL P 375 " --> pdb=" O   PRO P 371 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 383 through 396
      removed outlier: 4.336A  pdb=" N   HIS P 396 " --> pdb=" O   ILE P 392 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 406 through 418
      removed outlier: 3.555A  pdb=" N   LYS P 418 " --> pdb=" O   LYS P 414 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 420 through 442
      removed outlier: 3.640A  pdb=" N   CYS P 424 " --> pdb=" O   ILE P 420 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU P 425 " --> pdb=" O   ARG P 421 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER P 437 " --> pdb=" O   SER P 433 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ARG P 440 " --> pdb=" O   ILE P 436 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 443 through 447
    Processing helix  chain 'P' and resid 452 through 482
      removed outlier: 4.300A  pdb=" N   GLY P 469 " --> pdb=" O   ARG P 465 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   ARG P 470 " --> pdb=" O   GLU P 466 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU P 482 " --> pdb=" O   LEU P 478 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 502 through 508
      removed outlier: 3.757A  pdb=" N   MET P 506 " --> pdb=" O   ARG P 502 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 511 through 516
      removed outlier: 4.673A  pdb=" N   GLN P 515 " --> pdb=" O   THR P 511 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 609 through 624
    Processing helix  chain 'P' and resid 654 through 689
      Proline residue:  P 682  - end of helix
    Processing helix  chain 'P' and resid 690 through 699
    Processing helix  chain 'P' and resid 700 through 708
      removed outlier: 3.597A  pdb=" N   CYS P 708 " --> pdb=" O   ASN P 704 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 710 through 715
      removed outlier: 3.909A  pdb=" N   MET P 715 " --> pdb=" O   GLN P 711 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 718 through 747
      removed outlier: 3.754A  pdb=" N   ALA P 722 " --> pdb=" O   SER P 718 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR P 747 " --> pdb=" O   GLY P 743 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 75
    Processing sheet with id=AA2, first strand: chain 'B' and resid 73 through 75
      removed outlier: 6.653A  pdb=" N   ILE B  34 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLN B  33 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   LEU B 172 " --> pdb=" O   GLN B  33 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ALA B  35 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B  35 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   VAL B  37 " --> pdb=" O   VAL B 174 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   ILE B 201 " --> pdb=" O   CYS B 169 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   VAL B 203 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   ALA B 173 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   THR B 205 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   SER B 175 " --> pdb=" O   THR B 205 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 565 through 566
      removed outlier: 3.825A  pdb=" N   LYS B 539 " --> pdb=" O   ILE B 528 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR B 527 " --> pdb=" O   ALA B 606 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   LEU B 603 " --> pdb=" O   LEU B 588 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 80 through 83
      removed outlier: 6.586A  pdb=" N   ILE P  34 " --> pdb=" O   VAL P 135 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL P 174 " --> pdb=" O   VAL P  37 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   ILE P 201 " --> pdb=" O   CYS P 169 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE P 171 " --> pdb=" O   ILE P 201 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL P 203 " --> pdb=" O   ILE P 171 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ALA P 173 " --> pdb=" O   VAL P 203 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   THR P 205 " --> pdb=" O   ALA P 173 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   SER P 175 " --> pdb=" O   THR P 205 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 565 through 566
      removed outlier: 3.700A  pdb=" N   LYS P 539 " --> pdb=" O   ILE P 528 " (cutoff:3.500A)

    586 hydrogen bonds defined for protein.
    1701 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: 4.13

  Time building geometry restraints manager: 3.82 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 2082
        1.28 -     1.42: 2843
        1.42 -     1.56: 7123
        1.56 -     1.70: 10
        1.70 -     1.84: 122
  Bond restraints: 12180
  Sorted by residual:
  bond pdb=" C3' GCP B 801 "
       pdb=" C4' GCP B 801 "
    ideal  model  delta    sigma   weight residual
    1.526  1.292  0.234 2.00e-02 2.50e+03 1.37e+02
  bond pdb=" C3' GCP P 801 "
       pdb=" C4' GCP P 801 "
    ideal  model  delta    sigma   weight residual
    1.526  1.293  0.233 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" C4' GCP P 801 "
       pdb=" O4' GCP P 801 "
    ideal  model  delta    sigma   weight residual
    1.429  1.620 -0.191 2.00e-02 2.50e+03 9.11e+01
  bond pdb=" C4' GCP B 801 "
       pdb=" O4' GCP B 801 "
    ideal  model  delta    sigma   weight residual
    1.429  1.619 -0.190 2.00e-02 2.50e+03 9.04e+01
  bond pdb=" C3' GCP P 801 "
       pdb=" O3' GCP P 801 "
    ideal  model  delta    sigma   weight residual
    1.401  1.562 -0.161 2.00e-02 2.50e+03 6.52e+01
  ... (remaining 12175 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 16128
        2.83 -     5.66: 229
        5.66 -     8.49: 41
        8.49 -    11.32: 14
       11.32 -    14.15: 4
  Bond angle restraints: 16416
  Sorted by residual:
  angle pdb=" C   SER B 582 "
        pdb=" N   LYS B 583 "
        pdb=" CA  LYS B 583 "
      ideal   model   delta    sigma   weight residual
     121.70  133.09  -11.39 1.80e+00 3.09e-01 4.00e+01
  angle pdb=" C   SER P 582 "
        pdb=" N   LYS P 583 "
        pdb=" CA  LYS P 583 "
      ideal   model   delta    sigma   weight residual
     121.70  132.97  -11.27 1.80e+00 3.09e-01 3.92e+01
  angle pdb=" C   GLU P 717 "
        pdb=" N   SER P 718 "
        pdb=" CA  SER P 718 "
      ideal   model   delta    sigma   weight residual
     121.70  131.71  -10.01 1.80e+00 3.09e-01 3.09e+01
  angle pdb=" C   GLU B 717 "
        pdb=" N   SER B 718 "
        pdb=" CA  SER B 718 "
      ideal   model   delta    sigma   weight residual
     121.70  131.04   -9.34 1.80e+00 3.09e-01 2.69e+01
  angle pdb=" C   PHE B 317 "
        pdb=" N   ARG B 318 "
        pdb=" CA  ARG B 318 "
      ideal   model   delta    sigma   weight residual
     121.70  130.04   -8.34 1.80e+00 3.09e-01 2.15e+01
  ... (remaining 16411 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 7170
       16.47 -    32.94: 311
       32.94 -    49.42: 70
       49.42 -    65.89: 22
       65.89 -    82.36: 13
  Dihedral angle restraints: 7586
    sinusoidal: 3266
      harmonic: 4320
  Sorted by residual:
  dihedral pdb=" CA  ARG P 364 "
           pdb=" C   ARG P 364 "
           pdb=" N   ILE P 365 "
           pdb=" CA  ILE P 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" CA  GLU B 368 "
           pdb=" C   GLU B 368 "
           pdb=" N   ARG B 369 "
           pdb=" CA  ARG B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.99   21.01     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  ARG B 290 "
           pdb=" C   ARG B 290 "
           pdb=" N   ASP B 291 "
           pdb=" CA  ASP B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.31  -20.69     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 7583 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1082
       0.038 -    0.077: 539
       0.077 -    0.115: 167
       0.115 -    0.153: 38
       0.153 -    0.191: 4
  Chirality restraints: 1830
  Sorted by residual:
  chirality pdb=" C2' GCP B 801 "
            pdb=" C1' GCP B 801 "
            pdb=" C3' GCP B 801 "
            pdb=" O2' GCP B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.56   -0.19 2.00e-01 2.50e+01 9.14e-01
  chirality pdb=" C2' GCP P 801 "
            pdb=" C1' GCP P 801 "
            pdb=" C3' GCP P 801 "
            pdb=" O2' GCP P 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.56   -0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" CA  VAL B 544 "
            pdb=" N   VAL B 544 "
            pdb=" C   VAL B 544 "
            pdb=" CB  VAL B 544 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.13e-01
  ... (remaining 1827 not shown)

  Planarity restraints: 2135
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 432 "   -0.012 2.00e-02 2.50e+03   2.31e-02 5.35e+00
        pdb=" C   ILE B 432 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ILE B 432 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 433 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU P 330 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   LEU P 330 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   LEU P 330 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLN P 331 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 430 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.34e+00
        pdb=" C   MET B 430 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   MET B 430 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL B 431 "    0.011 2.00e-02 2.50e+03
  ... (remaining 2132 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.54: 61
        2.54 -     3.13: 9582
        3.13 -     3.72: 17654
        3.72 -     4.31: 23917
        4.31 -     4.90: 39446
  Nonbonded interactions: 90660
  Sorted by model distance:
  nonbonded pdb=" O1B GCP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     1.944 2.170
  nonbonded pdb=" OG1 THR B  65 "
            pdb="MG    MG B 802 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" OG1 THR P  65 "
            pdb="MG    MG P 802 "
     model   vdw
     2.002 2.170
  nonbonded pdb=" OE2 GLU B 104 "
            pdb=" NH2 ARG B 107 "
     model   vdw
     2.025 3.120
  nonbonded pdb=" O2G GCP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.035 2.170
  ... (remaining 90655 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 7 through 747 or resid 801 through 802))
  selection = (chain 'P' and (resid 7 through 20 or resid 29 through 747 or resid 801 through  \ 
802))
}

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:             1344.350
  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:          0.540
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.950
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.060
  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:4.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total: 1383.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
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      :  0.009   0.234  12181  Z= 0.398
  Angle     :  0.945  14.147  16416  Z= 0.488
  Chirality :  0.048   0.191   1830
  Planarity :  0.004   0.031   2135
  Dihedral  : 11.137  82.361   4782
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.10 %
    Favored  : 96.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.78 (0.19), residues: 1475
  helix: -0.90 (0.18), residues: 695
  sheet: -1.67 (0.34), residues: 184
  loop : -3.02 (0.19), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP B 616 
 HIS   0.009   0.002   HIS P 396 
 PHE   0.022   0.002   PHE B 366 
 TYR   0.022   0.002   TYR B 669 
 ARG   0.009   0.001   ARG B 724 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15298 (  584)
  hydrogen bonds       : angle       6.48159 ( 1701)
  covalent geometry    : bond        0.00866 (12180)
  covalent geometry    : angle       0.94506 (16416)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 227
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  361 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6722 (tpp-160)
REVERT: B  434 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7828 (tm-30)
REVERT: B  480 ASP cc_start: 0.8008 (m-30) cc_final: 0.7681 (m-30)
REVERT: B  648 MET cc_start: 0.4195 (mpp) cc_final: 0.3877 (mpp)
REVERT: B  681 MET cc_start: 0.7568 (ppp) cc_final: 0.7262 (tmm)
REVERT: P    1 MET cc_start: 0.7218 (mtt) cc_final: 0.7014 (mtp)
REVERT: P  181 LEU cc_start: 0.8820 (tp) cc_final: 0.8592 (tt)
REVERT: P  297 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7642 (ttm-80)
REVERT: P  356 LEU cc_start: 0.7181 (tt) cc_final: 0.6587 (mt)
REVERT: P  376 LYS cc_start: 0.7929 (ttpt) cc_final: 0.7659 (ttpp)
REVERT: P  489 ASN cc_start: 0.7964 (t0) cc_final: 0.7252 (p0)
REVERT: P  506 MET cc_start: -0.0395 (tpt) cc_final: -0.0913 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2894
  time to fit residues: 91.7759
Evaluate side-chains
  124 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 111 optimal weight:    0.0050
   chunk 61 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:   30.0000
   chunk 115 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0870
   chunk 85 optimal weight:    0.9980
   chunk 133 optimal weight:   30.0000
   overall best weight:    0.5972

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

Flipped N/Q/H residues before XYZ refinement:
B 178 ASN
B 284 GLN
B 288 HIS
B 733 HIS
P 155 GLN
P 278 GLN
** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 530 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.142456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.109713 restraints weight = 27869.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.110601 restraints weight = 16894.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111382 restraints weight = 11673.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12181  Z= 0.140
  Angle     :  0.657  12.011  16416  Z= 0.345
  Chirality :  0.042   0.167   1830
  Planarity :  0.004   0.038   2135
  Dihedral  :  6.992  88.066   1679
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  7.63 %
    Favored  : 91.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.20), residues: 1475
  helix:  0.25 (0.19), residues: 722
  sheet: -1.28 (0.37), residues: 178
  loop : -2.60 (0.21), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 616 
 HIS   0.005   0.001   HIS B 288 
 PHE   0.015   0.001   PHE P  83 
 TYR   0.012   0.001   TYR B 265 
 ARG   0.007   0.000   ARG B 657 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  584)
  hydrogen bonds       : angle       4.61217 ( 1701)
  covalent geometry    : bond        0.00291 (12180)
  covalent geometry    : angle       0.65659 (16416)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 1.364 
Fit side-chains
   revert: symmetry clash
REVERT: B   30 ASP cc_start: 0.7172 (t0) cc_final: 0.6955 (t0)
REVERT: B  648 MET cc_start: 0.4220 (mpp) cc_final: 0.3774 (mpp)
REVERT: B  657 ARG cc_start: 0.6585 (ptt-90) cc_final: 0.6201 (ptp90)
REVERT: B  681 MET cc_start: 0.7671 (ppp) cc_final: 0.7262 (tmm)
REVERT: B  728 MET cc_start: 0.7253 (OUTLIER) cc_final: 0.6952 (mtt)
REVERT: P  297 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7663 (ttm-80)
REVERT: P  361 ARG cc_start: 0.5515 (ttt90) cc_final: 0.4567 (ttm-80)
REVERT: P  489 ASN cc_start: 0.8158 (t0) cc_final: 0.7455 (p0)
REVERT: P  506 MET cc_start: -0.0546 (tpt) cc_final: -0.0984 (tpp)
  outliers start: 18
  outliers final: 9
  residues processed: 156
  average time/residue: 0.2355
  time to fit residues: 53.6498
Evaluate side-chains
  120 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  305 LEU
Chi-restraints excluded: chain P residue  329 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   chunk 120 optimal weight:    0.7980
   chunk 117 optimal weight:    0.9990
   chunk 142 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   chunk 135 optimal weight:    8.9990
   chunk 101 optimal weight:    3.9990
   chunk 143 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
P 178 ASN
** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.140220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.107286 restraints weight = 27703.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.106335 restraints weight = 18879.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.107783 restraints weight = 14144.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12181  Z= 0.141
  Angle     :  0.623  11.319  16416  Z= 0.329
  Chirality :  0.042   0.151   1830
  Planarity :  0.003   0.028   2135
  Dihedral  :  5.933  84.778   1679
  Min Nonbonded Distance : 1.889

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  :  9.37 %
    Favored  : 88.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.21), residues: 1475
  helix:  0.98 (0.20), residues: 703
  sheet: -1.02 (0.38), residues: 178
  loop : -2.16 (0.22), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 616 
 HIS   0.005   0.001   HIS P 367 
 PHE   0.013   0.001   PHE B 409 
 TYR   0.018   0.001   TYR P 354 
 ARG   0.007   0.000   ARG P 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  584)
  hydrogen bonds       : angle       4.18674 ( 1701)
  covalent geometry    : bond        0.00310 (12180)
  covalent geometry    : angle       0.62350 (16416)
  Misc. bond           : bond        0.00057 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 1.289 
Fit side-chains
REVERT: B  136 ASP cc_start: 0.7912 (t0) cc_final: 0.7532 (t0)
REVERT: B  361 ARG cc_start: 0.7533 (tpt-90) cc_final: 0.7238 (tpt-90)
REVERT: B  434 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7641 (tp30)
REVERT: B  486 MET cc_start: 0.7312 (tmm) cc_final: 0.6960 (tmm)
REVERT: B  648 MET cc_start: 0.4469 (mpp) cc_final: 0.3975 (mpp)
REVERT: P  184 SER cc_start: 0.9032 (OUTLIER) cc_final: 0.8426 (t)
REVERT: P  361 ARG cc_start: 0.5484 (ttt90) cc_final: 0.4642 (ttm110)
REVERT: P  506 MET cc_start: -0.0521 (tpt) cc_final: -0.0892 (tpp)
  outliers start: 32
  outliers final: 15
  residues processed: 152
  average time/residue: 0.2592
  time to fit residues: 56.2222
Evaluate side-chains
  123 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  745 ILE
Chi-restraints excluded: chain P residue   29 LEU
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  140 MET
Chi-restraints excluded: chain P residue  184 SER
Chi-restraints excluded: chain P residue  234 VAL
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  329 LEU
Chi-restraints excluded: chain P residue  330 LEU
Chi-restraints excluded: chain P residue  399 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 145 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 139 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9990
   chunk 135 optimal weight:   20.0000
   chunk 101 optimal weight:    2.9990
   chunk 130 optimal weight:   40.0000
   chunk 114 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
B 331 GLN
P  17 GLN
P 155 GLN
** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.140272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.107011 restraints weight = 27278.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.106460 restraints weight = 16589.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.106848 restraints weight = 13401.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12181  Z= 0.143
  Angle     :  0.611  11.372  16416  Z= 0.321
  Chirality :  0.042   0.151   1830
  Planarity :  0.003   0.028   2135
  Dihedral  :  5.858  84.988   1679
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 11.33 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.22), residues: 1475
  helix:  1.31 (0.20), residues: 707
  sheet: -0.93 (0.38), residues: 176
  loop : -2.08 (0.22), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 616 
 HIS   0.006   0.001   HIS P 367 
 PHE   0.013   0.001   PHE P 698 
 TYR   0.010   0.001   TYR P 314 
 ARG   0.006   0.000   ARG P 467 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03669 (  584)
  hydrogen bonds       : angle       4.00638 ( 1701)
  covalent geometry    : bond        0.00319 (12180)
  covalent geometry    : angle       0.61056 (16416)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.462 
Fit side-chains
REVERT: B  140 MET cc_start: 0.8198 (mtt) cc_final: 0.7993 (mtt)
REVERT: B  434 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8038 (tm-30)
REVERT: B  480 ASP cc_start: 0.8292 (m-30) cc_final: 0.7925 (m-30)
REVERT: B  486 MET cc_start: 0.7593 (tmm) cc_final: 0.7311 (tmm)
REVERT: B  648 MET cc_start: 0.4475 (mpp) cc_final: 0.4040 (mpp)
REVERT: P  361 ARG cc_start: 0.5317 (ttt90) cc_final: 0.4193 (ttm170)
REVERT: P  564 MET cc_start: 0.4484 (tpp) cc_final: 0.2877 (mmm)
  outliers start: 32
  outliers final: 14
  residues processed: 132
  average time/residue: 0.2689
  time to fit residues: 51.1324
Evaluate side-chains
  111 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  193 VAL
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  375 VAL
Chi-restraints excluded: chain B residue  580 MET
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  130 LEU
Chi-restraints excluded: chain P residue  140 MET
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 34 optimal weight:    0.0570
   chunk 82 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9980
   chunk 104 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 6 optimal weight:    0.8980
   chunk 80 optimal weight:    8.9990
   chunk 3 optimal weight:    0.5980
   chunk 121 optimal weight:    0.8980
   chunk 109 optimal weight:    4.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** P 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.141089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.108067 restraints weight = 27338.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.107315 restraints weight = 16331.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.108375 restraints weight = 13061.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.4241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12181  Z= 0.114
  Angle     :  0.575  11.330  16416  Z= 0.300
  Chirality :  0.040   0.147   1830
  Planarity :  0.003   0.028   2135
  Dihedral  :  5.639  84.958   1679
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.31 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.22), residues: 1475
  helix:  1.63 (0.20), residues: 706
  sheet: -0.81 (0.39), residues: 178
  loop : -2.02 (0.23), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 542 
 HIS   0.005   0.001   HIS P 367 
 PHE   0.009   0.001   PHE P 647 
 TYR   0.015   0.001   TYR B 125 
 ARG   0.004   0.000   ARG B 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03347 (  584)
  hydrogen bonds       : angle       3.83085 ( 1701)
  covalent geometry    : bond        0.00236 (12180)
  covalent geometry    : angle       0.57521 (16416)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.279 
Fit side-chains
REVERT: B  361 ARG cc_start: 0.7648 (tpt-90) cc_final: 0.6572 (tpp80)
REVERT: B  434 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7682 (tp30)
REVERT: B  486 MET cc_start: 0.7530 (tmm) cc_final: 0.7203 (tmm)
REVERT: B  648 MET cc_start: 0.4469 (mpp) cc_final: 0.4018 (mpp)
REVERT: P    6 MET cc_start: 0.8488 (tpp) cc_final: 0.8151 (tpp)
REVERT: P  361 ARG cc_start: 0.5241 (ttt90) cc_final: 0.4165 (ttm170)
REVERT: P  364 ARG cc_start: 0.6909 (ptm160) cc_final: 0.4787 (mtt90)
REVERT: P  564 MET cc_start: 0.4341 (tpp) cc_final: 0.2610 (mmm)
  outliers start: 22
  outliers final: 11
  residues processed: 125
  average time/residue: 0.2462
  time to fit residues: 44.8461
Evaluate side-chains
  112 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  365 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  580 MET
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  330 LEU
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  494 ILE
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 145 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0060
   chunk 144 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 25 optimal weight:    0.2980
   chunk 0 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 86 optimal weight:    7.9990
   chunk 50 optimal weight:   30.0000
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.8602

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

Flipped N/Q/H residues before XYZ refinement:
P 278 GLN
P 367 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.138331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.105874 restraints weight = 27885.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.104459 restraints weight = 21101.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.105147 restraints weight = 17788.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.4701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12181  Z= 0.155
  Angle     :  0.619  11.349  16416  Z= 0.321
  Chirality :  0.042   0.168   1830
  Planarity :  0.003   0.029   2135
  Dihedral  :  5.809  83.895   1679
  Min Nonbonded Distance : 1.931

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 11.86 %
    Favored  : 85.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.22), residues: 1475
  helix:  1.61 (0.20), residues: 709
  sheet: -0.73 (0.39), residues: 176
  loop : -1.93 (0.23), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 616 
 HIS   0.005   0.001   HIS P 396 
 PHE   0.010   0.001   PHE B 409 
 TYR   0.018   0.001   TYR B 125 
 ARG   0.005   0.000   ARG B 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  584)
  hydrogen bonds       : angle       3.94315 ( 1701)
  covalent geometry    : bond        0.00359 (12180)
  covalent geometry    : angle       0.61859 (16416)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 1.894 
Fit side-chains
REVERT: B  332 MET cc_start: 0.8447 (tpp) cc_final: 0.8169 (mmt)
REVERT: B  361 ARG cc_start: 0.7741 (tpt-90) cc_final: 0.6905 (tpt-90)
REVERT: B  434 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7803 (tp30)
REVERT: B  476 MET cc_start: 0.7869 (mmp) cc_final: 0.7147 (mmm)
REVERT: B  480 ASP cc_start: 0.8394 (m-30) cc_final: 0.8052 (m-30)
REVERT: B  486 MET cc_start: 0.7699 (tmm) cc_final: 0.7404 (tmm)
REVERT: B  648 MET cc_start: 0.4627 (mpp) cc_final: 0.4184 (mpp)
REVERT: P    6 MET cc_start: 0.8757 (tpp) cc_final: 0.8377 (tpp)
REVERT: P  361 ARG cc_start: 0.5733 (ttt90) cc_final: 0.4066 (ttt90)
REVERT: P  364 ARG cc_start: 0.7066 (ptm160) cc_final: 0.5187 (mtt90)
REVERT: P  564 MET cc_start: 0.4249 (tpp) cc_final: 0.2701 (mmm)
  outliers start: 31
  outliers final: 19
  residues processed: 118
  average time/residue: 0.3125
  time to fit residues: 54.4598
Evaluate side-chains
  108 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 LEU
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  291 ASP
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  580 MET
Chi-restraints excluded: chain B residue  685 ILE
Chi-restraints excluded: chain P residue   12 LEU
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  305 LEU
Chi-restraints excluded: chain P residue  330 LEU
Chi-restraints excluded: chain P residue  377 MET
Chi-restraints excluded: chain P residue  399 ARG
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  476 MET
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:   30.0000
   chunk 43 optimal weight:    0.9990
   chunk 136 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.139991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.107587 restraints weight = 27850.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.105826 restraints weight = 19077.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.107026 restraints weight = 15622.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12181  Z= 0.115
  Angle     :  0.584  11.374  16416  Z= 0.302
  Chirality :  0.040   0.147   1830
  Planarity :  0.003   0.029   2135
  Dihedral  :  5.584  82.287   1679
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.39 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.22), residues: 1475
  helix:  1.83 (0.20), residues: 711
  sheet: -0.69 (0.39), residues: 177
  loop : -1.84 (0.23), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 542 
 HIS   0.003   0.001   HIS P 396 
 PHE   0.008   0.001   PHE B 409 
 TYR   0.014   0.001   TYR B 125 
 ARG   0.008   0.000   ARG P 663 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03278 (  584)
  hydrogen bonds       : angle       3.76059 ( 1701)
  covalent geometry    : bond        0.00247 (12180)
  covalent geometry    : angle       0.58409 (16416)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 1.293 
Fit side-chains
REVERT: B  332 MET cc_start: 0.8409 (tpp) cc_final: 0.8103 (mmt)
REVERT: B  361 ARG cc_start: 0.7722 (tpt-90) cc_final: 0.6905 (tpt-90)
REVERT: B  377 MET cc_start: 0.7896 (ppp) cc_final: 0.7644 (ppp)
REVERT: B  434 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7777 (tp30)
REVERT: B  440 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8159 (mtm-85)
REVERT: B  521 ILE cc_start: -0.2195 (OUTLIER) cc_final: -0.2406 (mt)
REVERT: B  648 MET cc_start: 0.4576 (mpp) cc_final: 0.4145 (mpp)
REVERT: P    6 MET cc_start: 0.8673 (tpp) cc_final: 0.8385 (tpp)
REVERT: P  315 LYS cc_start: 0.8375 (mmmt) cc_final: 0.8066 (mmtt)
REVERT: P  361 ARG cc_start: 0.5743 (ttt90) cc_final: 0.4127 (ttt90)
REVERT: P  364 ARG cc_start: 0.6930 (ptm160) cc_final: 0.5330 (mtt90)
REVERT: P  564 MET cc_start: 0.4138 (tpp) cc_final: 0.2621 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2621
  time to fit residues: 41.0362
Evaluate side-chains
  106 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  659 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   78 THR
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  399 ARG
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  436 ILE
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 121 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0770
   chunk 105 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 128 optimal weight:    8.9990
   chunk 83 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0370
   chunk 78 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   overall best weight:    1.3820

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

Flipped N/Q/H residues before XYZ refinement:
P 288 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.138512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.106856 restraints weight = 28266.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.104659 restraints weight = 22291.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.105172 restraints weight = 20021.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.5184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12181  Z= 0.133
  Angle     :  0.603  11.345  16416  Z= 0.310
  Chirality :  0.041   0.158   1830
  Planarity :  0.003   0.030   2135
  Dihedral  :  5.614  82.269   1679
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.61 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.22), residues: 1475
  helix:  1.84 (0.20), residues: 713
  sheet: -0.64 (0.40), residues: 175
  loop : -1.80 (0.23), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 616 
 HIS   0.005   0.001   HIS P 396 
 PHE   0.007   0.001   PHE P  83 
 TYR   0.016   0.001   TYR B 125 
 ARG   0.005   0.000   ARG P 663 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03439 (  584)
  hydrogen bonds       : angle       3.75532 ( 1701)
  covalent geometry    : bond        0.00300 (12180)
  covalent geometry    : angle       0.60280 (16416)
  Misc. bond           : bond        0.00021 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 1.424 
Fit side-chains
REVERT: B  332 MET cc_start: 0.8489 (tpp) cc_final: 0.8247 (mmt)
REVERT: B  361 ARG cc_start: 0.7766 (tpt-90) cc_final: 0.6893 (tpt-90)
REVERT: B  434 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7884 (tp30)
REVERT: B  476 MET cc_start: 0.7917 (mmp) cc_final: 0.7122 (mmm)
REVERT: B  480 ASP cc_start: 0.8337 (m-30) cc_final: 0.7976 (m-30)
REVERT: B  521 ILE cc_start: -0.2003 (OUTLIER) cc_final: -0.2211 (mt)
REVERT: B  648 MET cc_start: 0.4329 (mpp) cc_final: 0.3871 (mpp)
REVERT: P    6 MET cc_start: 0.8756 (tpp) cc_final: 0.8514 (tpp)
REVERT: P  364 ARG cc_start: 0.6781 (ptm160) cc_final: 0.5174 (mtt90)
REVERT: P  648 MET cc_start: -0.0422 (mtp) cc_final: -0.0704 (mtt)
  outliers start: 19
  outliers final: 13
  residues processed: 103
  average time/residue: 0.2638
  time to fit residues: 39.7693
Evaluate side-chains
  100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  580 MET
Chi-restraints excluded: chain B residue  659 VAL
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  399 ARG
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 118 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 44 optimal weight:    0.0570
   chunk 48 optimal weight:    0.0980
   chunk 20 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 55 optimal weight:   20.0000
   chunk 54 optimal weight:   30.0000
   overall best weight:    0.5700

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.140277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.107640 restraints weight = 27541.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106714 restraints weight = 16199.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107331 restraints weight = 12991.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.5346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  12181  Z= 0.111
  Angle     :  0.591  11.385  16416  Z= 0.303
  Chirality :  0.040   0.143   1830
  Planarity :  0.003   0.031   2135
  Dihedral  :  5.411  80.848   1679
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.92 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.22), residues: 1475
  helix:  2.01 (0.20), residues: 713
  sheet: -0.61 (0.39), residues: 179
  loop : -1.75 (0.24), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 542 
 HIS   0.002   0.000   HIS P 396 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.012   0.001   TYR B 125 
 ARG   0.004   0.000   ARG P 663 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03143 (  584)
  hydrogen bonds       : angle       3.64935 ( 1701)
  covalent geometry    : bond        0.00232 (12180)
  covalent geometry    : angle       0.59105 (16416)
  Misc. bond           : bond        0.00002 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 1.397 
Fit side-chains
REVERT: B  332 MET cc_start: 0.8438 (tpp) cc_final: 0.8171 (mmt)
REVERT: B  434 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7766 (tp30)
REVERT: B  521 ILE cc_start: -0.1957 (OUTLIER) cc_final: -0.2176 (mt)
REVERT: B  648 MET cc_start: 0.4471 (mpp) cc_final: 0.3993 (mpp)
REVERT: P    6 MET cc_start: 0.8708 (tpp) cc_final: 0.8496 (tpp)
REVERT: P  218 ASP cc_start: 0.8282 (t0) cc_final: 0.8057 (t0)
REVERT: P  361 ARG cc_start: 0.5658 (ttt90) cc_final: 0.3776 (ttt90)
REVERT: P  364 ARG cc_start: 0.6548 (ptm160) cc_final: 0.5001 (mtt90)
REVERT: P  564 MET cc_start: 0.4092 (tmm) cc_final: 0.3255 (tpp)
REVERT: P  648 MET cc_start: -0.0334 (mtp) cc_final: -0.0641 (mtt)
  outliers start: 15
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2735
  time to fit residues: 42.6889
Evaluate side-chains
  105 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  506 MET
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  330 LEU
Chi-restraints excluded: chain P residue  399 ARG
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  436 ILE
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 138 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 57 optimal weight:   20.0000
   chunk 101 optimal weight:    8.9990
   chunk 99 optimal weight:    0.0770
   overall best weight:    2.0142

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.137797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.104233 restraints weight = 27342.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.103049 restraints weight = 16784.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.104602 restraints weight = 13726.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.5475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12181  Z= 0.158
  Angle     :  0.636  11.354  16416  Z= 0.326
  Chirality :  0.042   0.145   1830
  Planarity :  0.003   0.035   2135
  Dihedral  :  5.616  81.176   1679
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.14 %
    Favored  : 85.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.22), residues: 1475
  helix:  1.83 (0.20), residues: 718
  sheet: -0.49 (0.40), residues: 176
  loop : -1.79 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 616 
 HIS   0.005   0.001   HIS P 396 
 PHE   0.008   0.001   PHE P 647 
 TYR   0.016   0.001   TYR B 125 
 ARG   0.008   0.000   ARG P 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03540 (  584)
  hydrogen bonds       : angle       3.80561 ( 1701)
  covalent geometry    : bond        0.00368 (12180)
  covalent geometry    : angle       0.63551 (16416)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2950 Ramachandran restraints generated.
    1475 Oldfield, 0 Emsley, 1475 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 1.302 
Fit side-chains
REVERT: B  161 MET cc_start: 0.8417 (tpp) cc_final: 0.8054 (tpp)
REVERT: B  332 MET cc_start: 0.8513 (tpp) cc_final: 0.8287 (mmt)
REVERT: B  434 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7936 (tp30)
REVERT: B  476 MET cc_start: 0.7261 (mmm) cc_final: 0.6839 (mmp)
REVERT: B  480 ASP cc_start: 0.8395 (m-30) cc_final: 0.7916 (m-30)
REVERT: B  521 ILE cc_start: -0.1956 (OUTLIER) cc_final: -0.2177 (mt)
REVERT: B  648 MET cc_start: 0.4450 (mpp) cc_final: 0.3980 (mpp)
REVERT: P    6 MET cc_start: 0.8726 (tpp) cc_final: 0.8510 (tpp)
REVERT: P  364 ARG cc_start: 0.6830 (ptm160) cc_final: 0.5218 (mtt90)
REVERT: P  399 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.5188 (tpp-160)
REVERT: P  407 MET cc_start: 0.8553 (mmm) cc_final: 0.8316 (tpt)
REVERT: P  564 MET cc_start: 0.4097 (tmm) cc_final: 0.3256 (tpp)
  outliers start: 16
  outliers final: 14
  residues processed: 103
  average time/residue: 0.2852
  time to fit residues: 42.5619
Evaluate side-chains
  102 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  159 MET
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  506 MET
Chi-restraints excluded: chain B residue  521 ILE
Chi-restraints excluded: chain B residue  572 LEU
Chi-restraints excluded: chain B residue  670 MET
Chi-restraints excluded: chain P residue   64 VAL
Chi-restraints excluded: chain P residue   77 THR
Chi-restraints excluded: chain P residue  260 LEU
Chi-restraints excluded: chain P residue  266 ARG
Chi-restraints excluded: chain P residue  399 ARG
Chi-restraints excluded: chain P residue  434 GLU
Chi-restraints excluded: chain P residue  436 ILE
Chi-restraints excluded: chain P residue  603 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0870
   chunk 42 optimal weight:    0.5980
   chunk 115 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 145 optimal weight:    3.9990
   chunk 111 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 72 optimal weight:    3.9990
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.139926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.107111 restraints weight = 27532.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.106170 restraints weight = 16064.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107201 restraints weight = 13388.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.5610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  12181  Z= 0.113
  Angle     :  0.604  11.396  16416  Z= 0.310
  Chirality :  0.040   0.169   1830
  Planarity :  0.003   0.037   2135
  Dihedral  :  5.412  79.782   1679
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 13.22 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 1.75 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.22), residues: 1475
  helix:  2.03 (0.20), residues: 713
  sheet: -0.50 (0.40), residues: 175
  loop : -1.69 (0.24), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 542 
 HIS   0.003   0.000   HIS P 396 
 PHE   0.008   0.001   PHE B  94 
 TYR   0.012   0.001   TYR B 125 
 ARG   0.010   0.000   ARG P 440 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  584)
  hydrogen bonds       : angle       3.68145 ( 1701)
  covalent geometry    : bond        0.00238 (12180)
  covalent geometry    : angle       0.60427 (16416)
  Misc. bond           : bond        0.00003 (    1)

===============================================================================
Job complete
usr+sys time: 6443.09 seconds
wall clock time: 115 minutes 59.99 seconds (6959.99 seconds total)