Starting phenix.real_space_refine
on Tue Mar 11 15:31:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s86_19798/03_2025/8s86_19798.cif"
  }
  resolution = 2.8
  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=  -0.003 sd=   0.093
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3919      2.51       5
     N    1080      2.21       5
     O    1148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6177
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 392, 3085
          Classifications: {'peptide': 392}
          Link IDs: {'PTRANS': 22, 'TRANS': 369}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 3092
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 393, 3092
          Classifications: {'peptide': 393}
          Link IDs: {'PTRANS': 23, 'TRANS': 369}
          Chain breaks: 7
  Time building chain proxies: 4.45, per 1000 atoms: 0.72
  Number of scatterers: 6177
  At special positions: 0
  Unit cell: (71.06, 122.265, 72.105, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1148      8.00
     N    1080      7.00
     C    3919      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: 1.71
  Conformation dependent library (CDL) restraints added in 884.8 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1478

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      40.8% alpha, 21.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 130 through 135
    Processing helix  chain 'A' and resid 138 through 140
      No H-bonds generated for 'chain 'A' and resid 138 through 140'
    Processing helix  chain 'A' and resid 141 through 158
      removed outlier: 3.703A  pdb=" N   ALA A 155 " --> pdb=" O   LEU A 151 " (cutoff:3.500A)
      Proline residue:  A 156  - end of helix
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 191 through 196
    Processing helix  chain 'A' and resid 221 through 226
    Processing helix  chain 'A' and resid 237 through 255
      removed outlier: 3.736A  pdb=" N   ASP A 243 " --> pdb=" O   CYS A 239 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   LYS A 246 " --> pdb=" O   ARG A 242 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   TYR A 251 " --> pdb=" O   ILE A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 296 through 300
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 343 through 357
      removed outlier: 3.575A  pdb=" N   GLY A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 383
      removed outlier: 4.235A  pdb=" N   ALA A 376 " --> pdb=" O   PRO A 372 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   PHE A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 381 " --> pdb=" O   PHE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 438
      No H-bonds generated for 'chain 'A' and resid 436 through 438'
    Processing helix  chain 'A' and resid 454 through 470
      removed outlier: 3.655A  pdb=" N   SER A 458 " --> pdb=" O   GLY A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 484
    Processing helix  chain 'B' and resid 104 through 116
    Processing helix  chain 'B' and resid 130 through 135
    Processing helix  chain 'B' and resid 138 through 140
      No H-bonds generated for 'chain 'B' and resid 138 through 140'
    Processing helix  chain 'B' and resid 141 through 158
      removed outlier: 3.670A  pdb=" N   ALA B 155 " --> pdb=" O   LEU B 151 " (cutoff:3.500A)
      Proline residue:  B 156  - end of helix
    Processing helix  chain 'B' and resid 176 through 184
    Processing helix  chain 'B' and resid 191 through 197
    Processing helix  chain 'B' and resid 220 through 226
    Processing helix  chain 'B' and resid 237 through 255
      removed outlier: 3.798A  pdb=" N   ASP B 243 " --> pdb=" O   CYS B 239 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   LYS B 246 " --> pdb=" O   ARG B 242 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ILE B 247 " --> pdb=" O   ASP B 243 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA B 250 " --> pdb=" O   LYS B 246 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR B 251 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 296 through 300
    Processing helix  chain 'B' and resid 307 through 318
    Processing helix  chain 'B' and resid 343 through 356
    Processing helix  chain 'B' and resid 373 through 383
      removed outlier: 3.931A  pdb=" N   PHE B 377 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU B 381 " --> pdb=" O   PHE B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 438
      No H-bonds generated for 'chain 'B' and resid 436 through 438'
    Processing helix  chain 'B' and resid 454 through 470
      removed outlier: 3.670A  pdb=" N   SER B 458 " --> pdb=" O   GLY B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 484
      removed outlier: 3.734A  pdb=" N   GLY B 484 " --> pdb=" O   ASP B 481 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 88
      removed outlier: 3.511A  pdb=" N   PHE A 212 " --> pdb=" O   MET A 234 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   LEU A 120 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 7.930A  pdb=" N   ALA A 164 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ILE A 122 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 8.574A  pdb=" N   SER A 166 " --> pdb=" O   ILE A 122 " (cutoff:3.500A)
      removed outlier: 8.702A  pdb=" N   SER A 124 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   VAL A 161 " --> pdb=" O   GLN A 186 " (cutoff:3.500A)
      removed outlier: 8.361A  pdb=" N   ARG A 188 " --> pdb=" O   VAL A 161 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   ILE A 163 " --> pdb=" O   ARG A 188 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   VAL A 190 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL A 165 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 281
      removed outlier: 4.685A  pdb=" N   THR A 305 " --> pdb=" O   LEU A 292 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 279 through 281
      removed outlier: 4.626A  pdb=" N   LYS A 418 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ILE A 322 " --> pdb=" O   ARG A 361 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   LEU A 363 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A 324 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   SER A 365 " --> pdb=" O   VAL A 324 " (cutoff:3.500A)
      removed outlier: 7.690A  pdb=" N   VAL A 326 " --> pdb=" O   SER A 365 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   VAL A 360 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   LYS A 396 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   LEU A 362 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   PHE A 398 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE A 364 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 330
    Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 88
      removed outlier: 3.628A  pdb=" N   PHE B 212 " --> pdb=" O   MET B 234 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   LYS B 203 " --> pdb=" O   GLY B 215 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ARG B 162 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ALA B 164 " --> pdb=" O   ILE B 122 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B 166 " --> pdb=" O   SER B 124 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE B 163 " --> pdb=" O   ARG B 188 " (cutoff:3.500A)
      removed outlier: 7.532A  pdb=" N   VAL B 190 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL B 165 " --> pdb=" O   VAL B 190 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 279 through 281
      removed outlier: 4.618A  pdb=" N   THR B 305 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 281
      removed outlier: 4.589A  pdb=" N   LYS B 418 " --> pdb=" O   GLY B 429 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ILE B 322 " --> pdb=" O   ARG B 361 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   LEU B 363 " --> pdb=" O   ILE B 322 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   VAL B 324 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   SER B 365 " --> pdb=" O   VAL B 324 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   VAL B 326 " --> pdb=" O   SER B 365 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   VAL B 360 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LYS B 396 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   LEU B 362 " --> pdb=" O   LYS B 396 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE B 398 " --> pdb=" O   LEU B 362 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ILE B 364 " --> pdb=" O   PHE B 398 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 329 through 330

    270 hydrogen bonds defined for protein.
    717 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1527
        1.33 -     1.45: 1294
        1.45 -     1.57: 3459
        1.57 -     1.69: 1
        1.69 -     1.81: 46
  Bond restraints: 6327
  Sorted by residual:
  bond pdb=" N   ASN B 218 "
       pdb=" CA  ASN B 218 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.00e-02 1.00e+04 1.14e+01
  bond pdb=" CZ  ARG B 350 "
       pdb=" NH2 ARG B 350 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.46e+00
  bond pdb=" N   VAL B 227 "
       pdb=" CA  VAL B 227 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.036 1.18e-02 7.18e+03 9.27e+00
  bond pdb=" CZ  ARG A 350 "
       pdb=" NH2 ARG A 350 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.60e+00
  bond pdb=" N   ASP B 220 "
       pdb=" CA  ASP B 220 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.037 1.27e-02 6.20e+03 8.34e+00
  ... (remaining 6322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 7533
        1.66 -     3.32: 862
        3.32 -     4.99: 171
        4.99 -     6.65: 47
        6.65 -     8.31: 5
  Bond angle restraints: 8618
  Sorted by residual:
  angle pdb=" C   PRO B 296 "
        pdb=" N   PRO B 297 "
        pdb=" CA  PRO B 297 "
      ideal   model   delta    sigma   weight residual
     120.38  126.73   -6.35 1.03e+00 9.43e-01 3.80e+01
  angle pdb=" CA  ASP B 307 "
        pdb=" CB  ASP B 307 "
        pdb=" CG  ASP B 307 "
      ideal   model   delta    sigma   weight residual
     112.60  118.17   -5.57 1.00e+00 1.00e+00 3.10e+01
  angle pdb=" CA  ASP A 316 "
        pdb=" CB  ASP A 316 "
        pdb=" CG  ASP A 316 "
      ideal   model   delta    sigma   weight residual
     112.60  118.11   -5.51 1.00e+00 1.00e+00 3.03e+01
  angle pdb=" CB  HIS B 416 "
        pdb=" CG  HIS B 416 "
        pdb=" CD2 HIS B 416 "
      ideal   model   delta    sigma   weight residual
     131.20  124.45    6.75 1.30e+00 5.92e-01 2.69e+01
  angle pdb=" CA  TYR B 323 "
        pdb=" C   TYR B 323 "
        pdb=" N   VAL B 324 "
      ideal   model   delta    sigma   weight residual
     116.37  122.05   -5.68 1.19e+00 7.06e-01 2.28e+01
  ... (remaining 8613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 3395
       16.93 -    33.86: 275
       33.86 -    50.78: 64
       50.78 -    67.71: 7
       67.71 -    84.64: 4
  Dihedral angle restraints: 3745
    sinusoidal: 1465
      harmonic: 2280
  Sorted by residual:
  dihedral pdb=" CA  HIS B 337 "
           pdb=" C   HIS B 337 "
           pdb=" N   PRO B 338 "
           pdb=" CA  PRO B 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.02  -27.98     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  SER B  99 "
           pdb=" C   SER B  99 "
           pdb=" N   THR B 100 "
           pdb=" CA  THR B 100 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.47   27.53     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  ALA A 486 "
           pdb=" C   ALA A 486 "
           pdb=" N   CYS A 487 "
           pdb=" CA  CYS A 487 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.36  -25.64     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 3742 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 782
       0.084 -    0.167: 166
       0.167 -    0.251: 12
       0.251 -    0.335: 2
       0.335 -    0.418: 2
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" CA  ALA B 295 "
            pdb=" N   ALA B 295 "
            pdb=" C   ALA B 295 "
            pdb=" CB  ALA B 295 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.07    0.42 2.00e-01 2.50e+01 4.37e+00
  chirality pdb=" CA  ASP A 316 "
            pdb=" N   ASP A 316 "
            pdb=" C   ASP A 316 "
            pdb=" CB  ASP A 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.47e+00
  chirality pdb=" CA  TRP A 433 "
            pdb=" N   TRP A 433 "
            pdb=" C   TRP A 433 "
            pdb=" CB  TRP A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 961 not shown)

  Planarity restraints: 1107
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 433 "   -0.092 2.00e-02 2.50e+03   6.66e-02 1.11e+02
        pdb=" CG  TRP A 433 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 433 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 433 "    0.087 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 433 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 433 "    0.050 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 433 "    0.107 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 433 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 433 "   -0.026 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 433 "   -0.101 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 342 "    0.102 2.00e-02 2.50e+03   5.77e-02 8.32e+01
        pdb=" CG  TRP B 342 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 342 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 342 "   -0.068 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 342 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 342 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 342 "   -0.079 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 342 "    0.057 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 342 "   -0.013 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 342 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 433 "   -0.038 2.00e-02 2.50e+03   5.43e-02 7.38e+01
        pdb=" CG  TRP B 433 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 433 "   -0.074 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 433 "    0.073 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 433 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 433 "    0.058 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 433 "    0.072 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 433 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 433 "   -0.048 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 433 "   -0.078 2.00e-02 2.50e+03
  ... (remaining 1104 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1582
        2.81 -     3.34: 6174
        3.34 -     3.86: 10904
        3.86 -     4.38: 13688
        4.38 -     4.90: 21974
  Nonbonded interactions: 54322
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A  87 "
            pdb=" NH2 ARG A 466 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" NH1 ARG B 466 "
            pdb=" OD1 ASP B 467 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" NE1 TRP B 265 "
            pdb=" O   PRO B 298 "
     model   vdw
     2.338 3.120
  nonbonded pdb=" N   ASP B 191 "
            pdb=" OD1 ASP B 191 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" NH1 ARG A 466 "
            pdb=" OD1 ASP A 467 "
     model   vdw
     2.373 3.120
  ... (remaining 54317 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 'A' and (resid 79 through 386 or resid 388 through 389 or resid 391 throu \ 
gh 490))
  selection = (chain 'B' and (resid 79 through 256 or resid 265 through 334 or resid 338 throu \ 
gh 490))
}

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:             1.180
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     18.710
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  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:12.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6012
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      :  0.008   0.055   6327  Z= 0.497
  Angle     :  1.182   8.309   8618  Z= 0.770
  Chirality :  0.068   0.418    964
  Planarity :  0.013   0.142   1107
  Dihedral  : 13.436  84.640   2267
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  :  8.37 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.27 %
  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: -2.43 (0.26), residues: 759
  helix: -2.00 (0.23), residues: 266
  sheet: -0.09 (0.35), residues: 203
  loop : -2.22 (0.32), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.107   0.013   TRP A 433 
 HIS   0.018   0.002   HIS A 416 
 PHE   0.042   0.005   PHE B 377 
 TYR   0.103   0.010   TYR B 329 
 ARG   0.028   0.003   ARG A 424 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.6510 (tttp) cc_final: 0.6169 (pttp)
REVERT: A  234 MET cc_start: 0.7164 (ttm) cc_final: 0.6910 (tpp)
REVERT: A  276 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5404 (mt-10)
REVERT: B   94 ASP cc_start: 0.4739 (p0) cc_final: 0.4536 (p0)
REVERT: B  107 GLN cc_start: 0.7357 (mt0) cc_final: 0.7094 (mt0)
REVERT: B  276 GLU cc_start: 0.5716 (mm-30) cc_final: 0.5192 (pt0)
REVERT: B  340 ARG cc_start: 0.6052 (mmm-85) cc_final: 0.5406 (tpp80)
  outliers start: 15
  outliers final: 1
  residues processed: 147
  average time/residue: 1.0013
  time to fit residues: 155.5837
Evaluate side-chains
  93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  463 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 59 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 160 ASN
A 201 HIS
A 284 ASN
A 485 ASN
B 117 HIS
B 197 HIS
B 201 HIS
B 218 ASN
** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 416 HIS
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.189051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.170089 restraints weight = 6320.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 1.77
r_work: 0.4422 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4300 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6288
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6327  Z= 0.255
  Angle     :  0.701   9.155   8618  Z= 0.363
  Chirality :  0.047   0.174    964
  Planarity :  0.005   0.045   1107
  Dihedral  :  5.379  18.949    850
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 15.55 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.29), residues: 759
  helix: -0.44 (0.29), residues: 271
  sheet:  0.27 (0.36), residues: 201
  loop : -1.30 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 205 
 HIS   0.007   0.001   HIS A 416 
 PHE   0.019   0.003   PHE B 204 
 TYR   0.023   0.002   TYR B 291 
 ARG   0.003   0.000   ARG B 356 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.645 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.4940 (p0) cc_final: 0.4739 (p0)
REVERT: A  100 THR cc_start: 0.3447 (OUTLIER) cc_final: 0.3214 (p)
REVERT: A  167 LYS cc_start: 0.6332 (tttp) cc_final: 0.5985 (pttp)
REVERT: A  276 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5906 (mt-10)
REVERT: A  294 SER cc_start: 0.4663 (p) cc_final: 0.4430 (m)
REVERT: B   94 ASP cc_start: 0.4737 (p0) cc_final: 0.4464 (p0)
REVERT: B  327 MET cc_start: 0.5965 (ttt) cc_final: 0.5668 (tpp)
REVERT: B  346 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6326 (m-30)
  outliers start: 21
  outliers final: 3
  residues processed: 118
  average time/residue: 1.0407
  time to fit residues: 129.7766
Evaluate side-chains
  90 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0770
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 416 HIS
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.186375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.166610 restraints weight = 6402.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.4467 rms_B_bonded: 1.88
r_work: 0.4373 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.4248 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6327  Z= 0.258
  Angle     :  0.663   8.462   8618  Z= 0.343
  Chirality :  0.045   0.154    964
  Planarity :  0.005   0.044   1107
  Dihedral  :  5.003  20.707    848
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 14.80 %
    Favored  : 79.82 %
  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: -0.67 (0.29), residues: 759
  helix: -0.06 (0.30), residues: 265
  sheet:  0.31 (0.37), residues: 197
  loop : -1.21 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 205 
 HIS   0.009   0.001   HIS A 416 
 PHE   0.023   0.003   PHE B 212 
 TYR   0.027   0.003   TYR B 273 
 ARG   0.010   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 93
  time to evaluate  : 0.621 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3549 (OUTLIER) cc_final: 0.3334 (p)
REVERT: A  180 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5469 (mp)
REVERT: A  242 ARG cc_start: 0.6298 (ttm110) cc_final: 0.5966 (ttm110)
REVERT: A  277 THR cc_start: 0.7147 (p) cc_final: 0.6896 (p)
REVERT: A  294 SER cc_start: 0.4583 (p) cc_final: 0.4380 (m)
REVERT: B   94 ASP cc_start: 0.4916 (p0) cc_final: 0.4616 (p0)
REVERT: B  104 SER cc_start: 0.5675 (m) cc_final: 0.5282 (p)
REVERT: B  272 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6396 (pmm-80)
REVERT: B  277 THR cc_start: 0.7172 (p) cc_final: 0.6964 (p)
REVERT: B  327 MET cc_start: 0.5741 (ttt) cc_final: 0.5539 (tpp)
REVERT: B  340 ARG cc_start: 0.6566 (mmm160) cc_final: 0.5988 (tpt170)
REVERT: B  346 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6383 (m-30)
REVERT: B  371 GLU cc_start: 0.6425 (OUTLIER) cc_final: 0.5904 (pm20)
  outliers start: 36
  outliers final: 12
  residues processed: 121
  average time/residue: 0.9759
  time to fit residues: 125.4368
Evaluate side-chains
  99 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 44 optimal weight:    0.1980
   chunk 71 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
B 160 ASN
** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.185433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.165390 restraints weight = 6499.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.4447 rms_B_bonded: 1.90
r_work: 0.4354 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4227 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.4227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6437
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6327  Z= 0.269
  Angle     :  0.655   7.586   8618  Z= 0.341
  Chirality :  0.046   0.152    964
  Planarity :  0.005   0.044   1107
  Dihedral  :  4.949  19.511    848
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 16.14 %
    Favored  : 78.92 %
  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: -0.62 (0.30), residues: 759
  helix: -0.08 (0.30), residues: 277
  sheet:  0.33 (0.37), residues: 195
  loop : -1.15 (0.35), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 205 
 HIS   0.007   0.001   HIS A 416 
 PHE   0.027   0.003   PHE A 398 
 TYR   0.035   0.003   TYR A 291 
 ARG   0.004   0.000   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.654 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3583 (OUTLIER) cc_final: 0.3361 (p)
REVERT: A  180 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5478 (mp)
REVERT: A  242 ARG cc_start: 0.6185 (ttm110) cc_final: 0.5902 (ttm110)
REVERT: B   94 ASP cc_start: 0.4933 (p0) cc_final: 0.4593 (p0)
REVERT: B  104 SER cc_start: 0.5701 (m) cc_final: 0.5343 (p)
REVERT: B  272 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6465 (pmm-80)
REVERT: B  277 THR cc_start: 0.7169 (p) cc_final: 0.6965 (p)
REVERT: B  340 ARG cc_start: 0.6448 (mmm160) cc_final: 0.5532 (ttp-170)
REVERT: B  346 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6255 (m-30)
REVERT: B  371 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5860 (mp0)
REVERT: B  420 MET cc_start: 0.6541 (ttp) cc_final: 0.6276 (ttm)
  outliers start: 33
  outliers final: 11
  residues processed: 110
  average time/residue: 0.9766
  time to fit residues: 114.4755
Evaluate side-chains
  94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.647 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  371 GLU
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
B 160 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.183639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.163908 restraints weight = 6446.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.4433 rms_B_bonded: 1.87
r_work: 0.4342 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.4215 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6327  Z= 0.299
  Angle     :  0.687   7.542   8618  Z= 0.355
  Chirality :  0.047   0.213    964
  Planarity :  0.005   0.041   1107
  Dihedral  :  5.052  20.251    848
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 17.64 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.61 (0.30), residues: 759
  helix: -0.08 (0.30), residues: 272
  sheet:  0.31 (0.37), residues: 194
  loop : -1.09 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 205 
 HIS   0.006   0.001   HIS A 416 
 PHE   0.033   0.003   PHE A 398 
 TYR   0.027   0.003   TYR A 291 
 ARG   0.003   0.000   ARG A 272 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 82
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3667 (OUTLIER) cc_final: 0.3439 (p)
REVERT: A  246 LYS cc_start: 0.5355 (ttpt) cc_final: 0.4850 (ttpt)
REVERT: B   94 ASP cc_start: 0.5031 (p0) cc_final: 0.4703 (p0)
REVERT: B  104 SER cc_start: 0.6149 (m) cc_final: 0.5787 (p)
REVERT: B  180 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5092 (mp)
REVERT: B  272 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.6458 (pmm-80)
REVERT: B  346 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6275 (m-30)
REVERT: B  420 MET cc_start: 0.6411 (ttp) cc_final: 0.6178 (ttm)
  outliers start: 36
  outliers final: 16
  residues processed: 109
  average time/residue: 0.8908
  time to fit residues: 103.6593
Evaluate side-chains
  94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  305 THR
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    0.0870
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** A 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
B 117 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4631 r_free = 0.4631 target = 0.185794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.166719 restraints weight = 6440.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.4460 rms_B_bonded: 1.80
r_work: 0.4372 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.4249 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.4249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
moved from start:          0.3918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6327  Z= 0.238
  Angle     :  0.643   6.952   8618  Z= 0.332
  Chirality :  0.046   0.153    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.784  17.597    848
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 19.58 %
    Favored  : 75.78 %
  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: -0.42 (0.30), residues: 759
  helix:  0.10 (0.31), residues: 272
  sheet:  0.28 (0.37), residues: 201
  loop : -0.93 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 205 
 HIS   0.006   0.001   HIS B 117 
 PHE   0.031   0.003   PHE B 398 
 TYR   0.029   0.002   TYR A 291 
 ARG   0.007   0.000   ARG B 242 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 78
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3589 (OUTLIER) cc_final: 0.3384 (p)
REVERT: A  160 ASN cc_start: 0.7118 (t0) cc_final: 0.6296 (m-40)
REVERT: A  180 LEU cc_start: 0.5942 (OUTLIER) cc_final: 0.5366 (mp)
REVERT: A  208 ASP cc_start: 0.7447 (m-30) cc_final: 0.7117 (m-30)
REVERT: A  246 LYS cc_start: 0.5021 (ttpt) cc_final: 0.4529 (ttpt)
REVERT: A  346 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6319 (m-30)
REVERT: B   94 ASP cc_start: 0.5036 (p0) cc_final: 0.4679 (p0)
REVERT: B  180 LEU cc_start: 0.5967 (OUTLIER) cc_final: 0.5257 (mp)
REVERT: B  272 ARG cc_start: 0.6693 (OUTLIER) cc_final: 0.6467 (pmm-80)
REVERT: B  305 THR cc_start: 0.6953 (OUTLIER) cc_final: 0.6715 (m)
REVERT: B  346 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6222 (m-30)
REVERT: B  408 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6547 (mtt-85)
  outliers start: 31
  outliers final: 13
  residues processed: 102
  average time/residue: 0.7857
  time to fit residues: 86.3879
Evaluate side-chains
  92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  322 ILE
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  207 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  272 ARG
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0970
   chunk 58 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0470
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0870
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.2654

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
A 275 GLN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
B 201 HIS
B 218 ASN
** B 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.190693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.171537 restraints weight = 6293.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.4506 rms_B_bonded: 1.79
r_work: 0.4420 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4300 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.4300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6350
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6327  Z= 0.189
  Angle     :  0.609   8.345   8618  Z= 0.313
  Chirality :  0.045   0.153    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.540  16.278    848
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 20.48 %
    Favored  : 76.08 %
  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: -0.18 (0.30), residues: 759
  helix:  0.30 (0.31), residues: 269
  sheet:  0.36 (0.37), residues: 201
  loop : -0.73 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 205 
 HIS   0.005   0.001   HIS B 117 
 PHE   0.021   0.002   PHE B 398 
 TYR   0.030   0.002   TYR B 291 
 ARG   0.014   0.001   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.667 
Fit side-chains
REVERT: A  160 ASN cc_start: 0.7020 (t0) cc_final: 0.6249 (m-40)
REVERT: A  180 LEU cc_start: 0.5886 (OUTLIER) cc_final: 0.5384 (mp)
REVERT: A  208 ASP cc_start: 0.7424 (m-30) cc_final: 0.7094 (m-30)
REVERT: A  346 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6370 (m-30)
REVERT: B   94 ASP cc_start: 0.4965 (p0) cc_final: 0.4625 (p0)
REVERT: B  180 LEU cc_start: 0.5868 (OUTLIER) cc_final: 0.5188 (mp)
REVERT: B  340 ARG cc_start: 0.6304 (mmm160) cc_final: 0.5887 (tpt170)
REVERT: B  346 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6513 (m-30)
REVERT: B  408 ARG cc_start: 0.6724 (mtt90) cc_final: 0.6520 (mtt-85)
  outliers start: 23
  outliers final: 8
  residues processed: 95
  average time/residue: 0.7955
  time to fit residues: 81.3148
Evaluate side-chains
  81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0370
   chunk 27 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   chunk 74 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** A 415 ASN ** 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 = 0.4665 r_free = 0.4665 target = 0.189183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.169968 restraints weight = 6303.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.4486 rms_B_bonded: 1.77
r_work: 0.4400 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4279 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.4279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6327  Z= 0.228
  Angle     :  0.636   9.041   8618  Z= 0.324
  Chirality :  0.046   0.201    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.570  16.322    848
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.38 %
    Favored  : 75.64 %
  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: -0.13 (0.31), residues: 759
  helix:  0.39 (0.32), residues: 266
  sheet:  0.31 (0.37), residues: 202
  loop : -0.68 (0.37), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 205 
 HIS   0.003   0.001   HIS A 416 
 PHE   0.025   0.003   PHE B 398 
 TYR   0.029   0.002   TYR B 291 
 ARG   0.010   0.000   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A  160 ASN cc_start: 0.6958 (t0) cc_final: 0.6190 (m-40)
REVERT: A  180 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5278 (mp)
REVERT: A  208 ASP cc_start: 0.7379 (m-30) cc_final: 0.7035 (m-30)
REVERT: A  246 LYS cc_start: 0.4990 (ttpt) cc_final: 0.4552 (tmmt)
REVERT: A  374 MET cc_start: 0.6232 (ptm) cc_final: 0.5947 (ptp)
REVERT: B   94 ASP cc_start: 0.5011 (p0) cc_final: 0.4684 (p0)
REVERT: B  180 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5178 (mp)
REVERT: B  340 ARG cc_start: 0.6328 (mmm160) cc_final: 0.6049 (mmm160)
REVERT: B  346 ASP cc_start: 0.6891 (OUTLIER) cc_final: 0.6201 (m-30)
REVERT: B  408 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6547 (mtt-85)
  outliers start: 20
  outliers final: 11
  residues processed: 87
  average time/residue: 0.9004
  time to fit residues: 83.8178
Evaluate side-chains
  83 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0030
   chunk 31 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 18 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 41 optimal weight:    0.3980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.3348

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
A 416 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4693 r_free = 0.4693 target = 0.191995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.172589 restraints weight = 6344.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.4515 rms_B_bonded: 1.78
r_work: 0.4430 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.4309 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6307
moved from start:          0.4292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6327  Z= 0.196
  Angle     :  0.608   8.094   8618  Z= 0.313
  Chirality :  0.045   0.160    964
  Planarity :  0.005   0.041   1107
  Dihedral  :  4.462  15.679    848
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.82 %
    Favored  : 75.64 %
  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: -0.02 (0.31), residues: 759
  helix:  0.48 (0.32), residues: 266
  sheet:  0.45 (0.37), residues: 200
  loop : -0.69 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 468 
 HIS   0.005   0.001   HIS A 416 
 PHE   0.020   0.002   PHE B 398 
 TYR   0.032   0.002   TYR B 273 
 ARG   0.008   0.000   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A  160 ASN cc_start: 0.7046 (t0) cc_final: 0.6294 (m-40)
REVERT: A  180 LEU cc_start: 0.5830 (OUTLIER) cc_final: 0.5332 (mp)
REVERT: A  208 ASP cc_start: 0.7386 (m-30) cc_final: 0.7058 (m-30)
REVERT: A  346 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6272 (m-30)
REVERT: A  374 MET cc_start: 0.6402 (ptm) cc_final: 0.6046 (ptp)
REVERT: A  476 LEU cc_start: 0.6901 (tp) cc_final: 0.6378 (mt)
REVERT: B   94 ASP cc_start: 0.4984 (p0) cc_final: 0.4636 (p0)
REVERT: B  180 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5255 (mp)
REVERT: B  340 ARG cc_start: 0.6332 (mmm160) cc_final: 0.6045 (mmm160)
REVERT: B  346 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6479 (m-30)
  outliers start: 17
  outliers final: 10
  residues processed: 92
  average time/residue: 0.8144
  time to fit residues: 80.5390
Evaluate side-chains
  81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0980
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.4380

-------------------------------------------------------------------------------
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 = 0.4687 r_free = 0.4687 target = 0.191364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.171963 restraints weight = 6395.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 1.80
r_work: 0.4424 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4301 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6369
moved from start:          0.4320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6327  Z= 0.218
  Angle     :  0.631   8.529   8618  Z= 0.323
  Chirality :  0.046   0.172    964
  Planarity :  0.005   0.042   1107
  Dihedral  :  4.534  16.082    848
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.97 %
    Favored  : 75.78 %
  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:  0.02 (0.31), residues: 759
  helix:  0.52 (0.32), residues: 266
  sheet:  0.46 (0.37), residues: 200
  loop : -0.65 (0.37), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 468 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.020   0.002   PHE B 398 
 TYR   0.045   0.002   TYR B 273 
 ARG   0.008   0.000   ARG B 340 

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.697 
Fit side-chains
REVERT: A  160 ASN cc_start: 0.7223 (t0) cc_final: 0.6548 (m-40)
REVERT: A  180 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5425 (mp)
REVERT: A  208 ASP cc_start: 0.7296 (m-30) cc_final: 0.6990 (m-30)
REVERT: A  246 LYS cc_start: 0.5141 (ttpt) cc_final: 0.4737 (tmmt)
REVERT: A  272 ARG cc_start: 0.6486 (mpp-170) cc_final: 0.5974 (ttt-90)
REVERT: A  346 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6327 (m-30)
REVERT: A  374 MET cc_start: 0.6491 (ptm) cc_final: 0.6132 (ptp)
REVERT: A  476 LEU cc_start: 0.6817 (tp) cc_final: 0.6280 (mt)
REVERT: B   94 ASP cc_start: 0.4959 (p0) cc_final: 0.4644 (p0)
REVERT: B  180 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5325 (mp)
REVERT: B  340 ARG cc_start: 0.6350 (mmm160) cc_final: 0.6105 (mmm160)
REVERT: B  346 ASP cc_start: 0.6953 (OUTLIER) cc_final: 0.6285 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 85
  average time/residue: 1.0176
  time to fit residues: 92.9027
Evaluate side-chains
  81 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  180 LEU
Chi-restraints excluded: chain A residue  279 MET
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  243 ASP
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  490 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0040
   chunk 77 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.4170

-------------------------------------------------------------------------------
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 = 0.4694 r_free = 0.4694 target = 0.191949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.172363 restraints weight = 6419.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 1.81
r_work: 0.4424 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4299 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6327  Z= 0.210
  Angle     :  0.627   8.245   8618  Z= 0.322
  Chirality :  0.046   0.170    964
  Planarity :  0.005   0.040   1107
  Dihedral  :  4.484  16.580    848
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 14.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 21.67 %
    Favored  : 75.64 %
  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:  0.06 (0.31), residues: 759
  helix:  0.69 (0.33), residues: 260
  sheet:  0.39 (0.37), residues: 200
  loop : -0.68 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 468 
 HIS   0.004   0.001   HIS A 416 
 PHE   0.019   0.002   PHE B 398 
 TYR   0.027   0.002   TYR B 291 
 ARG   0.008   0.000   ARG B 340 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5958.92 seconds
wall clock time: 101 minutes 57.24 seconds (6117.24 seconds total)