Starting phenix.real_space_refine
on Thu Mar 13 14:14:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p4x_17429/03_2025/8p4x_17429.cif"
  }
  resolution = 2.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.189
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       4      5.49       5
     Mg      2      5.21       5
     S      78      5.16       5
     C    5564      2.51       5
     N    1456      2.21       5
     O    1652      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8756
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4282
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 526, 4282
          Classifications: {'peptide': 526}
          Link IDs: {'PTRANS': 39, 'TRANS': 486}
    Chain: "A"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 54
          Unusual residues: {' MG': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.71, per 1000 atoms: 0.99
  Number of scatterers: 8756
  At special positions: 0
  Unit cell: (95.682, 104.302, 95.682, 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      78     16.00
     P       4     15.00
     Mg      2     11.99
     O    1652      8.00
     N    1456      7.00
     C    5564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 2 sheets defined
      56.7% alpha, 4.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 77 through 99
      removed outlier: 3.626A  pdb=" N   LYS A  97 " --> pdb=" O   ASP A  93 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   HIS A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 121
      removed outlier: 4.228A  pdb=" N   LYS A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 134
      No H-bonds generated for 'chain 'A' and resid 132 through 134'
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 3.663A  pdb=" N   ASP A 139 " --> pdb=" O   TRP A 135 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A 141 " --> pdb=" O   PRO A 137 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASP A 144 " --> pdb=" O   LYS A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 171
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 3.871A  pdb=" N   LEU A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLY A 190 " --> pdb=" O   THR A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.762A  pdb=" N   LYS A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.528A  pdb=" N   GLY A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
      removed outlier: 3.710A  pdb=" N   GLU A 234 " --> pdb=" O   CYS A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 265
    Processing helix  chain 'A' and resid 283 through 290
    Processing helix  chain 'A' and resid 293 through 309
      removed outlier: 3.559A  pdb=" N   HIS A 302 " --> pdb=" O   TYR A 298 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 318
      removed outlier: 3.646A  pdb=" N   LEU A 317 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR A 318 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 314 through 318'
    Processing helix  chain 'A' and resid 319 through 331
      removed outlier: 3.880A  pdb=" N   TRP A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ARG A 324 " --> pdb=" O   GLN A 320 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET A 330 " --> pdb=" O   TYR A 326 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   SER A 331 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 364
    Processing helix  chain 'A' and resid 368 through 381
      removed outlier: 3.555A  pdb=" N   CYS A 374 " --> pdb=" O   TRP A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 397
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.845A  pdb=" N   GLY A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A 411 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 432
      removed outlier: 4.093A  pdb=" N   ALA A 425 " --> pdb=" O   TRP A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 3.909A  pdb=" N   CYS A 442 " --> pdb=" O   CYS A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 456
    Processing helix  chain 'A' and resid 459 through 466
      removed outlier: 3.614A  pdb=" N   TYR A 465 " --> pdb=" O   PHE A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 470
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.625A  pdb=" N   ALA A 483 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 492
    Processing helix  chain 'A' and resid 505 through 524
      removed outlier: 3.588A  pdb=" N   SER A 511 " --> pdb=" O   LYS A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 544
      removed outlier: 3.536A  pdb=" N   VAL A 540 " --> pdb=" O   ASP A 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 53
    Processing helix  chain 'B' and resid 77 through 99
      removed outlier: 3.627A  pdb=" N   LYS B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   HIS B  98 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 121
      removed outlier: 4.228A  pdb=" N   LYS B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 134
      No H-bonds generated for 'chain 'B' and resid 132 through 134'
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 3.663A  pdb=" N   ASP B 139 " --> pdb=" O   TRP B 135 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B 141 " --> pdb=" O   PRO B 137 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   VAL B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ASP B 144 " --> pdb=" O   LYS B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 171
    Processing helix  chain 'B' and resid 178 through 190
      removed outlier: 3.871A  pdb=" N   LEU B 188 " --> pdb=" O   GLN B 184 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU B 189 " --> pdb=" O   VAL B 185 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   GLY B 190 " --> pdb=" O   THR B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
      removed outlier: 3.763A  pdb=" N   LYS B 215 " --> pdb=" O   ASP B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 225
      removed outlier: 3.528A  pdb=" N   GLY B 225 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 235
      removed outlier: 3.709A  pdb=" N   GLU B 234 " --> pdb=" O   CYS B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 265
    Processing helix  chain 'B' and resid 283 through 290
    Processing helix  chain 'B' and resid 293 through 309
      removed outlier: 3.559A  pdb=" N   HIS B 302 " --> pdb=" O   TYR B 298 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL B 308 " --> pdb=" O   ASN B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 318
      removed outlier: 3.646A  pdb=" N   LEU B 317 " --> pdb=" O   LEU B 314 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR B 318 " --> pdb=" O   GLY B 315 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 314 through 318'
    Processing helix  chain 'B' and resid 319 through 331
      removed outlier: 3.881A  pdb=" N   TRP B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   ARG B 324 " --> pdb=" O   GLN B 320 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   GLU B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET B 330 " --> pdb=" O   TYR B 326 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 327 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 364
    Processing helix  chain 'B' and resid 368 through 381
      removed outlier: 3.556A  pdb=" N   CYS B 374 " --> pdb=" O   TRP B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 397
    Processing helix  chain 'B' and resid 404 through 416
      removed outlier: 3.844A  pdb=" N   GLY B 408 " --> pdb=" O   SER B 404 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   GLU B 410 " --> pdb=" O   VAL B 406 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   PHE B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 432
      removed outlier: 4.093A  pdb=" N   ALA B 425 " --> pdb=" O   TRP B 421 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 442
      removed outlier: 3.909A  pdb=" N   CYS B 442 " --> pdb=" O   CYS B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 456
    Processing helix  chain 'B' and resid 459 through 466
      removed outlier: 3.615A  pdb=" N   TYR B 465 " --> pdb=" O   PHE B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 470
    Processing helix  chain 'B' and resid 479 through 483
      removed outlier: 3.625A  pdb=" N   ALA B 483 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 492
    Processing helix  chain 'B' and resid 505 through 524
      removed outlier: 3.587A  pdb=" N   SER B 511 " --> pdb=" O   LYS B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 544
      removed outlier: 3.537A  pdb=" N   VAL B 540 " --> pdb=" O   ASP B 536 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106
      removed outlier: 6.299A  pdb=" N   VAL A  33 " --> pdb=" O   ARG A 124 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   THR A 126 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU A  35 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   GLU A 128 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 8.290A  pdb=" N   TRP A  37 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 106
      removed outlier: 6.300A  pdb=" N   VAL B  33 " --> pdb=" O   ARG B 124 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   THR B 126 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU B  35 " --> pdb=" O   THR B 126 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   GLU B 128 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   TRP B  37 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)

    340 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2744
        1.34 -     1.46: 2088
        1.46 -     1.58: 4014
        1.58 -     1.69: 4
        1.69 -     1.81: 114
  Bond restraints: 8964
  Sorted by residual:
  bond pdb=" O3P FAD A 601 "
       pdb=" P   FAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.660  1.585  0.075 2.00e-02 2.50e+03 1.42e+01
  bond pdb=" O3P FAD B 601 "
       pdb=" P   FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.660  1.585  0.075 2.00e-02 2.50e+03 1.41e+01
  bond pdb=" O5' FAD B 601 "
       pdb=" P   FAD B 601 "
    ideal  model  delta    sigma   weight residual
    1.637  1.574  0.063 2.00e-02 2.50e+03 9.95e+00
  bond pdb=" O5' FAD A 601 "
       pdb=" P   FAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.637  1.574  0.063 2.00e-02 2.50e+03 9.95e+00
  bond pdb=" O5B FAD A 601 "
       pdb=" PA  FAD A 601 "
    ideal  model  delta    sigma   weight residual
    1.634  1.572  0.062 2.00e-02 2.50e+03 9.49e+00
  ... (remaining 8959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 11902
        1.48 -     2.96: 221
        2.96 -     4.44: 60
        4.44 -     5.93: 5
        5.93 -     7.41: 6
  Bond angle restraints: 12194
  Sorted by residual:
  angle pdb=" O1P FAD B 601 "
        pdb=" P   FAD B 601 "
        pdb=" O2P FAD B 601 "
      ideal   model   delta    sigma   weight residual
     122.50  115.09    7.41 3.00e+00 1.11e-01 6.10e+00
  angle pdb=" O1P FAD A 601 "
        pdb=" P   FAD A 601 "
        pdb=" O2P FAD A 601 "
      ideal   model   delta    sigma   weight residual
     122.50  115.10    7.40 3.00e+00 1.11e-01 6.08e+00
  angle pdb=" O1A FAD B 601 "
        pdb=" PA  FAD B 601 "
        pdb=" O5B FAD B 601 "
      ideal   model   delta    sigma   weight residual
     104.10  111.17   -7.07 3.00e+00 1.11e-01 5.55e+00
  angle pdb=" O1A FAD A 601 "
        pdb=" PA  FAD A 601 "
        pdb=" O5B FAD A 601 "
      ideal   model   delta    sigma   weight residual
     104.10  111.16   -7.06 3.00e+00 1.11e-01 5.54e+00
  angle pdb=" O1A FAD B 601 "
        pdb=" PA  FAD B 601 "
        pdb=" O2A FAD B 601 "
      ideal   model   delta    sigma   weight residual
     121.20  114.74    6.46 3.00e+00 1.11e-01 4.64e+00
  ... (remaining 12189 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.12: 5002
       18.12 -    36.25: 212
       36.25 -    54.37: 62
       54.37 -    72.50: 30
       72.50 -    90.62: 12
  Dihedral angle restraints: 5318
    sinusoidal: 2270
      harmonic: 3048
  Sorted by residual:
  dihedral pdb=" CA  ARG B  39 "
           pdb=" C   ARG B  39 "
           pdb=" N   HIS B  40 "
           pdb=" CA  HIS B  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  ARG A  39 "
           pdb=" C   ARG A  39 "
           pdb=" N   HIS A  40 "
           pdb=" CA  HIS A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.28   16.72     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" O5' FAD A 601 "
           pdb=" O3P FAD A 601 "
           pdb=" P   FAD A 601 "
           pdb=" PA  FAD A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -61.77 -152.39   90.62     1      3.00e+01 1.11e-03 1.08e+01
  ... (remaining 5315 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 662
       0.025 -    0.049: 346
       0.049 -    0.074: 114
       0.074 -    0.098: 42
       0.098 -    0.123: 56
  Chirality restraints: 1220
  Sorted by residual:
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.77e-01
  chirality pdb=" CA  VAL B  33 "
            pdb=" N   VAL B  33 "
            pdb=" C   VAL B  33 "
            pdb=" CB  VAL B  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.68e-01
  chirality pdb=" C2B FAD A 601 "
            pdb=" C1B FAD A 601 "
            pdb=" C3B FAD A 601 "
            pdb=" O2B FAD A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.66    0.12 2.00e-01 2.50e+01 3.65e-01
  ... (remaining 1217 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 526 "    0.027 5.00e-02 4.00e+02   4.03e-02 2.60e+00
        pdb=" N   PRO B 527 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 527 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 527 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 526 "    0.027 5.00e-02 4.00e+02   4.02e-02 2.59e+00
        pdb=" N   PRO A 527 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 527 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 527 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 533 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO A 534 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 534 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 534 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 120
        2.67 -     3.23: 7683
        3.23 -     3.78: 12540
        3.78 -     4.34: 18624
        4.34 -     4.90: 30825
  Nonbonded interactions: 69792
  Sorted by model distance:
  nonbonded pdb=" O   HOH B 717 "
            pdb=" O   HOH B 740 "
     model   vdw
     2.112 3.040
  nonbonded pdb=" O   HOH A 717 "
            pdb=" O   HOH A 740 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OD2 ASP B 420 "
            pdb=" O   HOH B 701 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" OD2 ASP A 420 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.116 3.040
  nonbonded pdb=" NH1 ARG A 324 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.125 3.120
  ... (remaining 69787 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.560
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.220
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   8964  Z= 0.273
  Angle     :  0.561   7.407  12194  Z= 0.284
  Chirality :  0.040   0.123   1220
  Planarity :  0.004   0.040   1552
  Dihedral  : 13.116  90.621   3362
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 1.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1048
  helix:  0.99 (0.24), residues: 528
  sheet:  0.00 (0.58), residues: 70
  loop : -1.38 (0.27), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.012   0.001   PHE B 543 
 TYR   0.012   0.001   TYR B 326 
 ARG   0.003   0.000   ARG A  80 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A  115 GLN cc_start: 0.7079 (tt0) cc_final: 0.6857 (tt0)
REVERT: A  200 ASP cc_start: 0.7123 (t70) cc_final: 0.6896 (t0)
REVERT: B  115 GLN cc_start: 0.7076 (tt0) cc_final: 0.6854 (tt0)
REVERT: B  200 ASP cc_start: 0.7121 (t70) cc_final: 0.6893 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 1.3213
  time to fit residues: 203.9194
Evaluate side-chains
  127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 205 GLN
B 205 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.122246 restraints weight = 7942.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.66
r_work: 0.3123 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8964  Z= 0.222
  Angle     :  0.615   7.584  12194  Z= 0.311
  Chirality :  0.045   0.165   1220
  Planarity :  0.006   0.046   1552
  Dihedral  : 10.268  90.211   1232
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.42 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1048
  helix:  1.22 (0.24), residues: 528
  sheet:  0.21 (0.58), residues: 70
  loop : -1.21 (0.26), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 430 
 HIS   0.004   0.001   HIS A  45 
 PHE   0.014   0.002   PHE B 543 
 TYR   0.009   0.002   TYR A 326 
 ARG   0.003   0.001   ARG A 515 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  200 ASP cc_start: 0.7820 (t70) cc_final: 0.7594 (t0)
REVERT: A  235 LYS cc_start: 0.7910 (mtmp) cc_final: 0.7709 (mtmm)
REVERT: A  497 GLU cc_start: 0.8163 (pt0) cc_final: 0.7957 (pt0)
REVERT: B  200 ASP cc_start: 0.7817 (t70) cc_final: 0.7591 (t0)
  outliers start: 8
  outliers final: 2
  residues processed: 140
  average time/residue: 1.4867
  time to fit residues: 219.8510
Evaluate side-chains
  124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain B residue  110 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 81 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0010
   chunk 94 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.146052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.123136 restraints weight = 8706.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.51
r_work: 0.3300 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8964  Z= 0.161
  Angle     :  0.530   6.551  12194  Z= 0.265
  Chirality :  0.042   0.122   1220
  Planarity :  0.005   0.039   1552
  Dihedral  :  9.193  98.158   1232
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.64 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.26), residues: 1048
  helix:  1.30 (0.23), residues: 542
  sheet:  1.06 (0.60), residues: 66
  loop : -1.20 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.012   0.001   PHE A 543 
 TYR   0.008   0.001   TYR B 298 
 ARG   0.002   0.000   ARG A 281 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 1.156 
Fit side-chains
REVERT: A  188 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: A  341 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5457 (mp0)
REVERT: B  188 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8115 (mp)
REVERT: B  341 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5444 (mp0)
  outliers start: 16
  outliers final: 7
  residues processed: 134
  average time/residue: 1.6914
  time to fit residues: 238.6218
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  231 GLU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain B residue  490 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0980
   chunk 102 optimal weight:    4.9990
   chunk 48 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0570
   chunk 90 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 44 optimal weight:    0.3980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.148390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.125795 restraints weight = 8692.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3441 rms_B_bonded: 1.50
r_work: 0.3343 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8964  Z= 0.136
  Angle     :  0.488   6.164  12194  Z= 0.242
  Chirality :  0.040   0.122   1220
  Planarity :  0.004   0.037   1552
  Dihedral  :  8.187  99.640   1232
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 1.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.72 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1048
  helix:  1.50 (0.24), residues: 538
  sheet:  1.27 (0.60), residues: 66
  loop : -1.09 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.010   0.001   PHE A 543 
 TYR   0.007   0.001   TYR B 298 
 ARG   0.002   0.000   ARG A 281 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A  118 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6948 (mt-10)
REVERT: A  222 LYS cc_start: 0.6918 (mptt) cc_final: 0.6416 (mmmt)
REVERT: A  341 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5479 (mp0)
REVERT: B  118 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6935 (mt-10)
REVERT: B  222 LYS cc_start: 0.6905 (mptt) cc_final: 0.6412 (mmmt)
REVERT: B  341 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5472 (mp0)
  outliers start: 14
  outliers final: 4
  residues processed: 127
  average time/residue: 1.6612
  time to fit residues: 221.7958
Evaluate side-chains
  130 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 31 optimal weight:    0.0070
   chunk 51 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.146460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.123727 restraints weight = 8671.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.50
r_work: 0.3314 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8964  Z= 0.149
  Angle     :  0.514   6.844  12194  Z= 0.254
  Chirality :  0.041   0.118   1220
  Planarity :  0.004   0.036   1552
  Dihedral  :  8.377 104.447   1232
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 1.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 11.02 %
    Favored  : 87.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1048
  helix:  1.52 (0.24), residues: 538
  sheet:  1.26 (0.61), residues: 66
  loop : -1.04 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 430 
 HIS   0.003   0.001   HIS B  45 
 PHE   0.011   0.001   PHE B 543 
 TYR   0.008   0.001   TYR B 326 
 ARG   0.001   0.000   ARG A 281 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.036 
Fit side-chains
REVERT: A  118 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6919 (mt-10)
REVERT: A  152 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7456 (mmtm)
REVERT: A  188 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8024 (mp)
REVERT: A  341 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.5404 (mp0)
REVERT: B  118 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6917 (mt-10)
REVERT: B  152 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7447 (mmtm)
REVERT: B  188 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8017 (mp)
REVERT: B  341 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5417 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 126
  average time/residue: 1.7785
  time to fit residues: 235.1320
Evaluate side-chains
  136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  429 MET
Chi-restraints excluded: chain A residue  486 GLU
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  231 GLU
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain B residue  486 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 76 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  36 HIS
A 538 ASN
B  36 HIS
B 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.135805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.110556 restraints weight = 8476.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 1.59
r_work: 0.3087 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047   8964  Z= 0.476
  Angle     :  0.829  10.323  12194  Z= 0.427
  Chirality :  0.056   0.160   1220
  Planarity :  0.007   0.046   1552
  Dihedral  : 11.672 115.220   1232
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 11.34 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.24), residues: 1048
  helix:  0.65 (0.22), residues: 540
  sheet:  1.06 (0.61), residues: 66
  loop : -1.35 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP A 430 
 HIS   0.009   0.002   HIS A 385 
 PHE   0.020   0.003   PHE A 543 
 TYR   0.016   0.003   TYR B 465 
 ARG   0.009   0.001   ARG A  39 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 133
  time to evaluate  : 1.020 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7364 (p0)
REVERT: A  118 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7011 (mt-10)
REVERT: A  152 LYS cc_start: 0.7739 (mmtm) cc_final: 0.7368 (mmtm)
REVERT: A  188 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8087 (mp)
REVERT: A  341 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5600 (mp0)
REVERT: A  354 ASP cc_start: 0.6970 (t70) cc_final: 0.6761 (t70)
REVERT: A  356 GLU cc_start: 0.6990 (mp0) cc_final: 0.6721 (mp0)
REVERT: B  110 ASP cc_start: 0.7672 (OUTLIER) cc_final: 0.7372 (p0)
REVERT: B  118 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.7019 (mt-10)
REVERT: B  152 LYS cc_start: 0.7723 (mmtm) cc_final: 0.7353 (mmtm)
REVERT: B  188 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: B  341 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5560 (mp0)
REVERT: B  354 ASP cc_start: 0.6961 (t70) cc_final: 0.6750 (t70)
REVERT: B  356 GLU cc_start: 0.6970 (mp0) cc_final: 0.6698 (mp0)
  outliers start: 21
  outliers final: 8
  residues processed: 141
  average time/residue: 1.6281
  time to fit residues: 241.7170
Evaluate side-chains
  147 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  490 LYS
Chi-restraints excluded: chain A residue  497 GLU
Chi-restraints excluded: chain A residue  522 SER
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  341 GLU
Chi-restraints excluded: chain B residue  490 LYS
Chi-restraints excluded: chain B residue  497 GLU
Chi-restraints excluded: chain B residue  522 SER
Chi-restraints excluded: chain B residue  535 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 90 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0040
   chunk 21 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 47 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.142855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.118082 restraints weight = 8607.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.60
r_work: 0.3193 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8964  Z= 0.154
  Angle     :  0.548   7.880  12194  Z= 0.274
  Chirality :  0.041   0.140   1220
  Planarity :  0.005   0.039   1552
  Dihedral  :  9.634 106.860   1232
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.85 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.26), residues: 1048
  helix:  1.20 (0.23), residues: 542
  sheet:  1.22 (0.61), residues: 66
  loop : -1.20 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.011   0.001   PHE B 543 
 TYR   0.008   0.001   TYR B 326 
 ARG   0.002   0.000   ARG A 281 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 1.145 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8131 (ttpp) cc_final: 0.7801 (tttm)
REVERT: A  110 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7395 (p0)
REVERT: A  118 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6778 (mt-10)
REVERT: A  152 LYS cc_start: 0.7663 (mmtm) cc_final: 0.7321 (mmtm)
REVERT: A  188 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7983 (mp)
REVERT: A  222 LYS cc_start: 0.6913 (mptt) cc_final: 0.6260 (mmmt)
REVERT: A  341 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5298 (mp0)
REVERT: A  354 ASP cc_start: 0.6663 (t70) cc_final: 0.6423 (t70)
REVERT: B  110 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7397 (p0)
REVERT: B  118 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6801 (mt-10)
REVERT: B  152 LYS cc_start: 0.7687 (mmtm) cc_final: 0.7345 (mmtm)
REVERT: B  188 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7983 (mp)
REVERT: B  222 LYS cc_start: 0.6921 (mptt) cc_final: 0.6261 (mmmt)
REVERT: B  341 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5281 (mp0)
REVERT: B  354 ASP cc_start: 0.6677 (t70) cc_final: 0.6430 (t70)
  outliers start: 13
  outliers final: 1
  residues processed: 124
  average time/residue: 1.6807
  time to fit residues: 218.5736
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 93 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 538 ASN
B 136 GLN
B 538 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.113378 restraints weight = 8641.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.62
r_work: 0.3129 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8964  Z= 0.268
  Angle     :  0.657   8.655  12194  Z= 0.331
  Chirality :  0.046   0.158   1220
  Planarity :  0.006   0.041   1552
  Dihedral  : 10.516 114.161   1232
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 12.53 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.25), residues: 1048
  helix:  1.09 (0.23), residues: 540
  sheet:  1.14 (0.61), residues: 66
  loop : -1.30 (0.26), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 430 
 HIS   0.005   0.001   HIS A  45 
 PHE   0.015   0.002   PHE B 543 
 TYR   0.011   0.002   TYR B 465 
 ARG   0.004   0.000   ARG A  39 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A  110 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7410 (p0)
REVERT: A  188 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8021 (mp)
REVERT: A  341 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5302 (mp0)
REVERT: A  354 ASP cc_start: 0.6920 (t70) cc_final: 0.6701 (t70)
REVERT: A  356 GLU cc_start: 0.6933 (mp0) cc_final: 0.6681 (mp0)
REVERT: B   74 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7827 (tttm)
REVERT: B  110 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7441 (p0)
REVERT: B  188 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8017 (mp)
REVERT: B  341 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5275 (mp0)
REVERT: B  354 ASP cc_start: 0.6907 (t70) cc_final: 0.6679 (t70)
REVERT: B  356 GLU cc_start: 0.6896 (mp0) cc_final: 0.6630 (mp0)
  outliers start: 16
  outliers final: 3
  residues processed: 129
  average time/residue: 1.8123
  time to fit residues: 245.6355
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  497 GLU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.116555 restraints weight = 8617.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 1.62
r_work: 0.3188 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8964  Z= 0.184
  Angle     :  0.580   7.028  12194  Z= 0.292
  Chirality :  0.043   0.183   1220
  Planarity :  0.005   0.039   1552
  Dihedral  :  9.767 110.437   1232
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 1.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.07 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 1048
  helix:  1.25 (0.23), residues: 540
  sheet:  1.20 (0.62), residues: 66
  loop : -1.23 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.014   0.001   PHE A 543 
 TYR   0.009   0.001   TYR B 326 
 ARG   0.001   0.000   ARG B 389 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.253 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7764 (tttm)
REVERT: A  110 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7403 (p0)
REVERT: A  118 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6793 (mt-10)
REVERT: A  188 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7979 (mp)
REVERT: A  222 LYS cc_start: 0.6964 (mptt) cc_final: 0.6294 (ptmm)
REVERT: A  341 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5271 (mp0)
REVERT: A  356 GLU cc_start: 0.6825 (mp0) cc_final: 0.6573 (mp0)
REVERT: B  110 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7396 (p0)
REVERT: B  118 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6804 (mt-10)
REVERT: B  188 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7978 (mp)
REVERT: B  222 LYS cc_start: 0.6907 (mptt) cc_final: 0.6243 (ptmm)
REVERT: B  341 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5252 (mp0)
REVERT: B  356 GLU cc_start: 0.6783 (mp0) cc_final: 0.6527 (mp0)
  outliers start: 11
  outliers final: 2
  residues processed: 123
  average time/residue: 1.8548
  time to fit residues: 239.0131
Evaluate side-chains
  131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  118 GLU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  118 GLU
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   chunk 54 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 93 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.141976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.116816 restraints weight = 8608.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.64
r_work: 0.3186 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8964  Z= 0.172
  Angle     :  0.566   7.212  12194  Z= 0.282
  Chirality :  0.042   0.157   1220
  Planarity :  0.005   0.038   1552
  Dihedral  :  9.151 108.962   1232
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.07 %
    Favored  : 85.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1048
  helix:  1.34 (0.23), residues: 540
  sheet:  1.23 (0.62), residues: 66
  loop : -1.19 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 430 
 HIS   0.003   0.001   HIS A  45 
 PHE   0.013   0.001   PHE B 543 
 TYR   0.009   0.001   TYR B 326 
 ARG   0.001   0.000   ARG B 281 

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

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

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2096 Ramachandran restraints generated.
    1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 1.106 
Fit side-chains
REVERT: A   74 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7792 (tttm)
REVERT: A  110 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7392 (p0)
REVERT: A  188 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7917 (mp)
REVERT: A  222 LYS cc_start: 0.6861 (mptt) cc_final: 0.6256 (ptpp)
REVERT: A  341 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5255 (mp0)
REVERT: B   74 LYS cc_start: 0.8075 (ttpp) cc_final: 0.7772 (tttm)
REVERT: B  110 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.7395 (p0)
REVERT: B  188 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7914 (mp)
REVERT: B  222 LYS cc_start: 0.6859 (mptt) cc_final: 0.6263 (ptpp)
REVERT: B  341 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5218 (mp0)
REVERT: B  356 GLU cc_start: 0.6822 (mp0) cc_final: 0.6601 (mp0)
  outliers start: 12
  outliers final: 2
  residues processed: 122
  average time/residue: 1.8161
  time to fit residues: 233.4718
Evaluate side-chains
  133 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  341 GLU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain B residue  110 ASP
Chi-restraints excluded: chain B residue  188 LEU
Chi-restraints excluded: chain B residue  235 LYS
Chi-restraints excluded: chain B residue  341 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 4 optimal weight:    0.0170
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 98 optimal weight:    5.9990
   chunk 2 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0970
   chunk 9 optimal weight:    0.9980
   overall best weight:    1.0220

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

Flipped N/Q/H residues before XYZ refinement:
A 538 ASN
B 538 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.141611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.116771 restraints weight = 8556.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.60
r_work: 0.3178 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8964  Z= 0.188
  Angle     :  0.596   9.154  12194  Z= 0.296
  Chirality :  0.043   0.164   1220
  Planarity :  0.005   0.038   1552
  Dihedral  :  9.260 110.705   1232
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 2.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.28 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1048
  helix:  1.30 (0.23), residues: 540
  sheet:  1.22 (0.62), residues: 66
  loop : -1.19 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 430 
 HIS   0.004   0.001   HIS A  45 
 PHE   0.014   0.001   PHE A 543 
 TYR   0.010   0.001   TYR B 326 
 ARG   0.001   0.000   ARG B 389 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7269.00 seconds
wall clock time: 126 minutes 49.96 seconds (7609.96 seconds total)