Starting phenix.real_space_refine
on Wed Sep 17 06:35:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s86_19798/09_2025/8s86_19798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s86_19798/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s86_19798/09_2025/8s86_19798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s86_19798/09_2025/8s86_19798.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s86_19798/09_2025/8s86_19798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s86_19798/09_2025/8s86_19798.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.64, per 1000 atoms: 0.27
  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: 0.60
  Conformation dependent library (CDL) restraints added in 323.2 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.25
  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: 0.95

  Time building geometry restraints manager: 0.73 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:             1.610
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.930
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.820
-------------------------------------------------------------------------------
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= 0.464
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.028   0.003   ARG A 424 
 TYR   0.103   0.010   TYR B 329 
 PHE   0.042   0.005   PHE B 377 
 TRP   0.107   0.013   TRP A 433 
 HIS   0.018   0.002   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00752 ( 6327)
  covalent geometry    : angle       1.18208 ( 8618)
  hydrogen bonds       : bond        0.17393 (  262)
  hydrogen bonds       : angle       8.61172 (  717)

*********************** 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  : 0.224 
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: 0.4970
  time to fit residues: 76.8738
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  : 0.232 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4384

-------------------------------------------------------------------------------
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 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 485 ASN
B 117 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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.190555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.171436 restraints weight = 6387.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.4501 rms_B_bonded: 1.79
r_work: 0.4417 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4294 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.4294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6261
moved from start:          0.2444

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= 0.161
  Angle     :  0.692   8.968   8618  Z= 0.357
  Chirality :  0.046   0.176    964
  Planarity :  0.005   0.044   1107
  Dihedral  :  5.305  17.978    850
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 15.55 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.91 (0.29), residues: 759
  helix: -0.42 (0.29), residues: 271
  sheet:  0.25 (0.36), residues: 203
  loop : -1.29 (0.34), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 356 
 TYR   0.023   0.002   TYR B 291 
 PHE   0.017   0.003   PHE B 204 
 TRP   0.027   0.002   TRP B 205 
 HIS   0.007   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6327)
  covalent geometry    : angle       0.69174 ( 8618)
  hydrogen bonds       : bond        0.04564 (  262)
  hydrogen bonds       : angle       6.41816 (  717)

*********************** 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
  122 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.4866 (p0) cc_final: 0.4661 (p0)
REVERT: A  100 THR cc_start: 0.3429 (OUTLIER) cc_final: 0.3181 (p)
REVERT: A  167 LYS cc_start: 0.6354 (tttp) cc_final: 0.6009 (pttp)
REVERT: A  276 GLU cc_start: 0.6091 (mt-10) cc_final: 0.5856 (mt-10)
REVERT: A  294 SER cc_start: 0.4546 (p) cc_final: 0.4335 (m)
REVERT: B   94 ASP cc_start: 0.4736 (p0) cc_final: 0.4448 (p0)
REVERT: B  327 MET cc_start: 0.5959 (ttt) cc_final: 0.5656 (tpp)
REVERT: B  346 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6439 (m-30)
  outliers start: 20
  outliers final: 3
  residues processed: 116
  average time/residue: 0.5219
  time to fit residues: 63.7491
Evaluate side-chains
  87 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 82
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
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  291 TYR
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 55 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 41 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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
** 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 = 0.4635 r_free = 0.4635 target = 0.186365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.167064 restraints weight = 6386.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.4462 rms_B_bonded: 1.82
r_work: 0.4370 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4243 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.4243
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.3137

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= 0.178
  Angle     :  0.681   9.139   8618  Z= 0.351
  Chirality :  0.046   0.155    964
  Planarity :  0.005   0.044   1107
  Dihedral  :  5.052  19.638    848
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 15.10 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.29), residues: 759
  helix: -0.13 (0.30), residues: 271
  sheet:  0.27 (0.36), residues: 197
  loop : -1.21 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 340 
 TYR   0.028   0.003   TYR B 273 
 PHE   0.024   0.003   PHE B 212 
 TRP   0.017   0.002   TRP B 205 
 HIS   0.009   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6327)
  covalent geometry    : angle       0.68137 ( 8618)
  hydrogen bonds       : bond        0.04785 (  262)
  hydrogen bonds       : angle       6.32009 (  717)

*********************** 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
  125 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 THR cc_start: 0.3578 (OUTLIER) cc_final: 0.3376 (p)
REVERT: A  180 LEU cc_start: 0.6027 (OUTLIER) cc_final: 0.5542 (mp)
REVERT: A  242 ARG cc_start: 0.6311 (ttm110) cc_final: 0.6004 (ttm110)
REVERT: A  277 THR cc_start: 0.7173 (p) cc_final: 0.6924 (p)
REVERT: B   94 ASP cc_start: 0.4917 (p0) cc_final: 0.4609 (p0)
REVERT: B  104 SER cc_start: 0.5720 (m) cc_final: 0.5356 (p)
REVERT: B  272 ARG cc_start: 0.6671 (mpp-170) cc_final: 0.6383 (pmm-80)
REVERT: B  340 ARG cc_start: 0.6581 (mmm160) cc_final: 0.5993 (tpt170)
REVERT: B  346 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6409 (m-30)
REVERT: B  371 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5904 (pm20)
  outliers start: 33
  outliers final: 10
  residues processed: 119
  average time/residue: 0.4377
  time to fit residues: 55.2450
Evaluate side-chains
  96 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
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 B residue  207 VAL
Chi-restraints excluded: chain B residue  243 ASP
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  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 73 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    1.2386

-------------------------------------------------------------------------------
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 = 0.4561 r_free = 0.4561 target = 0.179371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.159502 restraints weight = 6532.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 1.87
r_work: 0.4295 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.4171 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6547
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   6327  Z= 0.262
  Angle     :  0.777   8.557   8618  Z= 0.400
  Chirality :  0.050   0.197    964
  Planarity :  0.005   0.045   1107
  Dihedral  :  5.488  21.965    848
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 20.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  5.98 %
    Allowed  : 16.89 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.28), residues: 759
  helix: -0.30 (0.29), residues: 266
  sheet:  0.06 (0.35), residues: 200
  loop : -1.38 (0.33), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 304 
 TYR   0.031   0.003   TYR A 291 
 PHE   0.035   0.004   PHE A 398 
 TRP   0.021   0.003   TRP B 205 
 HIS   0.008   0.002   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 6327)
  covalent geometry    : angle       0.77687 ( 8618)
  hydrogen bonds       : bond        0.05651 (  262)
  hydrogen bonds       : angle       6.63504 (  717)

*********************** 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
  127 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 87
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5135 (p0) cc_final: 0.4879 (p0)
REVERT: A  100 THR cc_start: 0.3559 (OUTLIER) cc_final: 0.3333 (p)
REVERT: A  180 LEU cc_start: 0.5863 (OUTLIER) cc_final: 0.5245 (mp)
REVERT: A  242 ARG cc_start: 0.6439 (ttm110) cc_final: 0.6182 (ttm110)
REVERT: A  465 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6412 (mm)
REVERT: B   94 ASP cc_start: 0.5140 (p0) cc_final: 0.4797 (p0)
REVERT: B  104 SER cc_start: 0.6134 (m) cc_final: 0.5708 (p)
REVERT: B  272 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6380 (pmm-80)
REVERT: B  327 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.4190 (tpt)
REVERT: B  340 ARG cc_start: 0.6336 (mmm160) cc_final: 0.5624 (ttp-170)
REVERT: B  371 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5907 (mp0)
REVERT: B  490 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5563 (tt)
  outliers start: 40
  outliers final: 15
  residues processed: 117
  average time/residue: 0.4215
  time to fit residues: 52.4573
Evaluate side-chains
  106 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 THR
Chi-restraints excluded: chain A residue  122 ILE
Chi-restraints excluded: chain A residue  180 LEU
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  458 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue  195 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  327 MET
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  490 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0870
   chunk 67 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0170
   chunk 62 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.4196

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4642 r_free = 0.4642 target = 0.186551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.167212 restraints weight = 6466.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 1.80
r_work: 0.4375 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.4250 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.4250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6327  Z= 0.148
  Angle     :  0.640   7.334   8618  Z= 0.331
  Chirality :  0.045   0.156    964
  Planarity :  0.005   0.042   1107
  Dihedral  :  4.889  17.384    848
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 19.28 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.30), residues: 759
  helix: -0.04 (0.31), residues: 272
  sheet:  0.25 (0.37), residues: 200
  loop : -1.05 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 272 
 TYR   0.028   0.002   TYR A 291 
 PHE   0.024   0.003   PHE B 398 
 TRP   0.014   0.002   TRP B 205 
 HIS   0.006   0.001   HIS A 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6327)
  covalent geometry    : angle       0.64028 ( 8618)
  hydrogen bonds       : bond        0.04134 (  262)
  hydrogen bonds       : angle       6.39771 (  717)

*********************** 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
  120 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 87
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5255 (p0) cc_final: 0.5006 (p0)
REVERT: A  100 THR cc_start: 0.3544 (OUTLIER) cc_final: 0.3318 (p)
REVERT: A  246 LYS cc_start: 0.5143 (ttpt) cc_final: 0.4431 (tmmt)
REVERT: A  346 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6287 (m-30)
REVERT: B   94 ASP cc_start: 0.5041 (p0) cc_final: 0.4692 (p0)
REVERT: B  104 SER cc_start: 0.5860 (m) cc_final: 0.5529 (p)
REVERT: B  272 ARG cc_start: 0.6697 (OUTLIER) cc_final: 0.6333 (pmm-80)
REVERT: B  273 TYR cc_start: 0.7339 (m-10) cc_final: 0.7086 (m-80)
REVERT: B  305 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6628 (m)
REVERT: B  346 ASP cc_start: 0.7019 (OUTLIER) cc_final: 0.6335 (m-30)
  outliers start: 33
  outliers final: 9
  residues processed: 112
  average time/residue: 0.4378
  time to fit residues: 51.9297
Evaluate side-chains
  94 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
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  294 SER
Chi-restraints excluded: chain A residue  327 MET
Chi-restraints excluded: chain A residue  346 ASP
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  279 MET
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  490 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
** 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 = 0.4617 r_free = 0.4617 target = 0.184529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.164867 restraints weight = 6398.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.4444 rms_B_bonded: 1.84
r_work: 0.4353 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4229 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.4229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.3909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6327  Z= 0.171
  Angle     :  0.678   9.418   8618  Z= 0.345
  Chirality :  0.047   0.209    964
  Planarity :  0.005   0.043   1107
  Dihedral  :  4.887  18.383    848
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 17.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 19.88 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.58 (0.30), residues: 759
  helix: -0.05 (0.30), residues: 272
  sheet:  0.26 (0.37), residues: 200
  loop : -1.06 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 242 
 TYR   0.028   0.003   TYR B 291 
 PHE   0.029   0.003   PHE A 398 
 TRP   0.014   0.002   TRP B 205 
 HIS   0.006   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 6327)
  covalent geometry    : angle       0.67824 ( 8618)
  hydrogen bonds       : bond        0.04363 (  262)
  hydrogen bonds       : angle       6.36409 (  717)

*********************** 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: 28
    poor density    : 81
  time to evaluate  : 0.207 
Fit side-chains
REVERT: A   94 ASP cc_start: 0.5405 (p0) cc_final: 0.5141 (p0)
REVERT: A  100 THR cc_start: 0.3571 (OUTLIER) cc_final: 0.3354 (p)
REVERT: A  136 THR cc_start: 0.6577 (p) cc_final: 0.6219 (t)
REVERT: A  160 ASN cc_start: 0.7026 (t0) cc_final: 0.6173 (m-40)
REVERT: A  246 LYS cc_start: 0.5263 (ttpt) cc_final: 0.4597 (tmmt)
REVERT: A  275 GLN cc_start: 0.5795 (OUTLIER) cc_final: 0.5554 (tt0)
REVERT: A  346 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6327 (m-30)
REVERT: B   94 ASP cc_start: 0.5069 (p0) cc_final: 0.4739 (p0)
REVERT: B  104 SER cc_start: 0.5976 (m) cc_final: 0.5769 (p)
REVERT: B  180 LEU cc_start: 0.5927 (OUTLIER) cc_final: 0.5222 (mp)
REVERT: B  272 ARG cc_start: 0.6677 (OUTLIER) cc_final: 0.6323 (pmm-80)
REVERT: B  305 THR cc_start: 0.6688 (OUTLIER) cc_final: 0.6478 (m)
REVERT: B  346 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6235 (m-30)
  outliers start: 28
  outliers final: 11
  residues processed: 102
  average time/residue: 0.4283
  time to fit residues: 46.5084
Evaluate side-chains
  91 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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  275 GLN
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  333 LEU
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  272 ARG
Chi-restraints excluded: chain B residue  279 MET
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  346 ASP
Chi-restraints excluded: chain B residue  380 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 31 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.183845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.164661 restraints weight = 6477.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.4433 rms_B_bonded: 1.80
r_work: 0.4344 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.4221 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.4221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.4043

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= 0.186
  Angle     :  0.691   9.141   8618  Z= 0.352
  Chirality :  0.047   0.186    964
  Planarity :  0.005   0.048   1107
  Dihedral  :  4.952  18.059    848
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 17.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  4.93 %
    Allowed  : 19.73 %
    Favored  : 75.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.30), residues: 759
  helix: -0.01 (0.30), residues: 269
  sheet:  0.25 (0.37), residues: 200
  loop : -1.04 (0.36), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 340 
 TYR   0.029   0.003   TYR B 291 
 PHE   0.028   0.003   PHE A 398 
 TRP   0.014   0.002   TRP B 205 
 HIS   0.006   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 6327)
  covalent geometry    : angle       0.69054 ( 8618)
  hydrogen bonds       : bond        0.04490 (  262)
  hydrogen bonds       : angle       6.41302 (  717)

*********************** 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
  109 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 76
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5513 (p0) cc_final: 0.5246 (p0)
REVERT: A  100 THR cc_start: 0.3722 (OUTLIER) cc_final: 0.3495 (p)
REVERT: A  136 THR cc_start: 0.6585 (p) cc_final: 0.6257 (t)
REVERT: A  180 LEU cc_start: 0.6009 (OUTLIER) cc_final: 0.5454 (mp)
REVERT: A  246 LYS cc_start: 0.5139 (OUTLIER) cc_final: 0.4526 (tmmt)
REVERT: A  275 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5995 (tt0)
REVERT: A  346 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6354 (m-30)
REVERT: B   94 ASP cc_start: 0.4989 (p0) cc_final: 0.4659 (p0)
REVERT: B  180 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5355 (mp)
REVERT: B  272 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6419 (pmm-80)
REVERT: B  327 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.4320 (tpt)
REVERT: B  340 ARG cc_start: 0.6344 (mmm160) cc_final: 0.6094 (mmm160)
REVERT: B  346 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6238 (m-30)
  outliers start: 33
  outliers final: 15
  residues processed: 101
  average time/residue: 0.4139
  time to fit residues: 44.5844
Evaluate side-chains
  95 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
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  246 LYS
Chi-restraints excluded: chain A residue  275 GLN
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  333 LEU
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  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  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  327 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0170
   chunk 20 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.5018

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.186156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.166741 restraints weight = 6515.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.4454 rms_B_bonded: 1.81
r_work: 0.4366 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.4242 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6357
moved from start:          0.4120

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= 0.157
  Angle     :  0.664   7.887   8618  Z= 0.340
  Chirality :  0.046   0.162    964
  Planarity :  0.005   0.049   1107
  Dihedral  :  4.819  18.868    848
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.08 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.30), residues: 759
  helix:  0.24 (0.31), residues: 260
  sheet:  0.26 (0.37), residues: 200
  loop : -0.91 (0.36), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 340 
 TYR   0.040   0.003   TYR B 273 
 PHE   0.022   0.003   PHE A 398 
 TRP   0.013   0.002   TRP B 205 
 HIS   0.005   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6327)
  covalent geometry    : angle       0.66391 ( 8618)
  hydrogen bonds       : bond        0.04096 (  262)
  hydrogen bonds       : angle       6.40414 (  717)

*********************** 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
  103 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5716 (p0) cc_final: 0.5455 (p0)
REVERT: A  100 THR cc_start: 0.3628 (OUTLIER) cc_final: 0.3377 (p)
REVERT: A  136 THR cc_start: 0.6562 (p) cc_final: 0.6210 (t)
REVERT: A  160 ASN cc_start: 0.7032 (t0) cc_final: 0.6014 (m-40)
REVERT: A  180 LEU cc_start: 0.5795 (OUTLIER) cc_final: 0.5240 (mp)
REVERT: A  246 LYS cc_start: 0.4932 (OUTLIER) cc_final: 0.4297 (tmmt)
REVERT: A  346 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6292 (m-30)
REVERT: A  374 MET cc_start: 0.6356 (ptm) cc_final: 0.6066 (ptp)
REVERT: B   94 ASP cc_start: 0.4985 (p0) cc_final: 0.4648 (p0)
REVERT: B  180 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5170 (mp)
REVERT: B  242 ARG cc_start: 0.6435 (mtt-85) cc_final: 0.6104 (ptp-110)
REVERT: B  305 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6709 (m)
REVERT: B  340 ARG cc_start: 0.6404 (mmm160) cc_final: 0.6113 (mmm160)
REVERT: B  346 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6396 (m-30)
  outliers start: 27
  outliers final: 13
  residues processed: 97
  average time/residue: 0.4068
  time to fit residues: 42.1139
Evaluate side-chains
  89 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
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  246 LYS
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  333 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  478 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  279 MET
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  490 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 2 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0050
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 275 GLN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 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 = 0.4651 r_free = 0.4651 target = 0.187796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.167956 restraints weight = 6373.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.4477 rms_B_bonded: 1.85
r_work: 0.4389 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.4265 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.4265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6405
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   6327  Z= 0.157
  Angle     :  0.666  12.787   8618  Z= 0.338
  Chirality :  0.047   0.220    964
  Planarity :  0.005   0.041   1107
  Dihedral  :  4.714  16.841    848
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.12 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.30), residues: 759
  helix:  0.23 (0.32), residues: 260
  sheet:  0.28 (0.37), residues: 195
  loop : -0.89 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 340 
 TYR   0.043   0.003   TYR B 273 
 PHE   0.020   0.003   PHE A 398 
 TRP   0.016   0.002   TRP B 468 
 HIS   0.006   0.001   HIS B 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6327)
  covalent geometry    : angle       0.66591 ( 8618)
  hydrogen bonds       : bond        0.04030 (  262)
  hydrogen bonds       : angle       6.47633 (  717)

*********************** 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
  95 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5702 (p0) cc_final: 0.5379 (p0)
REVERT: A  100 THR cc_start: 0.3629 (OUTLIER) cc_final: 0.3408 (p)
REVERT: A  136 THR cc_start: 0.6568 (p) cc_final: 0.6244 (t)
REVERT: A  160 ASN cc_start: 0.6959 (t0) cc_final: 0.6059 (m-40)
REVERT: A  180 LEU cc_start: 0.5885 (OUTLIER) cc_final: 0.5357 (mp)
REVERT: A  192 MET cc_start: 0.4309 (mtm) cc_final: 0.4040 (mtm)
REVERT: A  208 ASP cc_start: 0.7348 (m-30) cc_final: 0.7010 (m-30)
REVERT: A  246 LYS cc_start: 0.5066 (OUTLIER) cc_final: 0.4454 (tmmt)
REVERT: A  346 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6348 (m-30)
REVERT: A  374 MET cc_start: 0.6380 (ptm) cc_final: 0.6114 (ptp)
REVERT: B   94 ASP cc_start: 0.4951 (p0) cc_final: 0.4625 (p0)
REVERT: B  180 LEU cc_start: 0.5991 (OUTLIER) cc_final: 0.5279 (mp)
REVERT: B  305 THR cc_start: 0.6987 (OUTLIER) cc_final: 0.6744 (m)
REVERT: B  319 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7377 (mpt180)
REVERT: B  340 ARG cc_start: 0.6388 (mmm160) cc_final: 0.6116 (mmm160)
REVERT: B  346 ASP cc_start: 0.6945 (OUTLIER) cc_final: 0.6260 (m-30)
  outliers start: 22
  outliers final: 11
  residues processed: 91
  average time/residue: 0.4378
  time to fit residues: 42.4118
Evaluate side-chains
  88 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
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  246 LYS
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  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  319 ARG
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 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0470
   chunk 46 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0370
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
A 313 ASN
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS
** B 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4656 r_free = 0.4656 target = 0.188377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.168369 restraints weight = 6446.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.4474 rms_B_bonded: 1.87
r_work: 0.4386 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4263 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6399
moved from start:          0.4303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6327  Z= 0.157
  Angle     :  0.665  12.543   8618  Z= 0.339
  Chirality :  0.047   0.220    964
  Planarity :  0.005   0.039   1107
  Dihedral  :  4.681  16.378    848
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.38 %
    Favored  : 74.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.31), residues: 759
  helix:  0.30 (0.32), residues: 260
  sheet:  0.28 (0.37), residues: 199
  loop : -0.95 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 340 
 TYR   0.032   0.003   TYR B 273 
 PHE   0.023   0.003   PHE B 398 
 TRP   0.022   0.002   TRP A 468 
 HIS   0.006   0.001   HIS B 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6327)
  covalent geometry    : angle       0.66549 ( 8618)
  hydrogen bonds       : bond        0.03988 (  262)
  hydrogen bonds       : angle       6.50154 (  717)

********************** 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
  103 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 75
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ASP cc_start: 0.5674 (p0) cc_final: 0.5396 (p0)
REVERT: A  100 THR cc_start: 0.3661 (OUTLIER) cc_final: 0.3419 (p)
REVERT: A  136 THR cc_start: 0.6557 (p) cc_final: 0.6248 (t)
REVERT: A  160 ASN cc_start: 0.7000 (t0) cc_final: 0.6149 (m-40)
REVERT: A  180 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5404 (mp)
REVERT: A  208 ASP cc_start: 0.7370 (m-30) cc_final: 0.7045 (m-30)
REVERT: A  246 LYS cc_start: 0.5095 (OUTLIER) cc_final: 0.4483 (tmmt)
REVERT: A  346 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6336 (m-30)
REVERT: A  374 MET cc_start: 0.6353 (ptm) cc_final: 0.5964 (ptp)
REVERT: A  476 LEU cc_start: 0.7001 (tp) cc_final: 0.6491 (mt)
REVERT: B   94 ASP cc_start: 0.5056 (p0) cc_final: 0.4723 (p0)
REVERT: B  180 LEU cc_start: 0.5981 (OUTLIER) cc_final: 0.5309 (mp)
REVERT: B  305 THR cc_start: 0.6980 (OUTLIER) cc_final: 0.6739 (m)
REVERT: B  319 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7386 (mpt180)
REVERT: B  340 ARG cc_start: 0.6417 (mmm160) cc_final: 0.6152 (mmm160)
REVERT: B  346 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6269 (m-30)
  outliers start: 28
  outliers final: 14
  residues processed: 96
  average time/residue: 0.4412
  time to fit residues: 45.0429
Evaluate side-chains
  93 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
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  246 LYS
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  333 LEU
Chi-restraints excluded: chain A residue  346 ASP
Chi-restraints excluded: chain A residue  458 SER
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  279 MET
Chi-restraints excluded: chain B residue  294 SER
Chi-restraints excluded: chain B residue  305 THR
Chi-restraints excluded: chain B residue  319 ARG
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 39 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 46 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 57 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.4778

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

Flipped N/Q/H residues before XYZ refinement:
** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 117 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.189887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.170378 restraints weight = 6353.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.4492 rms_B_bonded: 1.78
r_work: 0.4407 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4284 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.4284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6327
moved from start:          0.4407

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= 0.153
  Angle     :  0.660  12.503   8618  Z= 0.336
  Chirality :  0.047   0.199    964
  Planarity :  0.005   0.039   1107
  Dihedral  :  4.669  16.414    848
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 16.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 22.42 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.31), residues: 759
  helix:  0.38 (0.32), residues: 260
  sheet:  0.28 (0.37), residues: 199
  loop : -0.97 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 242 
 TYR   0.029   0.002   TYR B 291 
 PHE   0.029   0.003   PHE B 398 
 TRP   0.025   0.002   TRP A 468 
 HIS   0.007   0.001   HIS B 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 6327)
  covalent geometry    : angle       0.66016 ( 8618)
  hydrogen bonds       : bond        0.03957 (  262)
  hydrogen bonds       : angle       6.47601 (  717)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2821.51 seconds
wall clock time: 48 minutes 52.60 seconds (2932.60 seconds total)