Starting phenix.real_space_refine
on Sat May 10 09:47:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgm_41241/05_2025/8tgm_41241_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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      58      5.16       5
     C    3878      2.51       5
     N     900      2.21       5
     O     990      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5826
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2869
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 21, 'TRANS': 362}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2869
          Classifications: {'peptide': 384}
          Link IDs: {'PTRANS': 21, 'TRANS': 362}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.18, per 1000 atoms: 0.89
  Number of scatterers: 5826
  At special positions: 0
  Unit cell: (73.04, 65.736, 114.872, 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      58     16.00
     O     990      8.00
     N     900      7.00
     C    3878      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.64
  Conformation dependent library (CDL) restraints added in 923.2 milliseconds
  

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      90.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.738A  pdb=" N   VAL A  25 " --> pdb=" O   GLN A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 54
    Processing helix  chain 'A' and resid 131 through 144
      removed outlier: 4.004A  pdb=" N   GLU A 135 " --> pdb=" O   PHE A 131 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   THR A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   ARG A 138 " --> pdb=" O   GLU A 134 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A 143 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   ALA A 144 " --> pdb=" O   GLY A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 165
      Proline residue:  A 155  - end of helix
      removed outlier: 4.369A  pdb=" N   GLY A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 166 through 187
    Processing helix  chain 'A' and resid 189 through 219
      removed outlier: 3.683A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 254
      removed outlier: 4.082A  pdb=" N   ARG A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ALA A 232 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   LEU A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 241 " --> pdb=" O   ALA A 237 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   VAL A 242 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
      removed outlier: 4.051A  pdb=" N   SER A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   VAL A 249 " --> pdb=" O   PRO A 245 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLU A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE A 253 " --> pdb=" O   VAL A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.533A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   CYS A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 297
    Processing helix  chain 'A' and resid 299 through 318
      removed outlier: 3.895A  pdb=" N   ALA A 305 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   GLY A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 4.660A  pdb=" N   VAL A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 330
    Processing helix  chain 'A' and resid 334 through 341
      removed outlier: 3.877A  pdb=" N   LEU A 338 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
      removed outlier: 4.638A  pdb=" N   GLY A 339 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
      removed outlier: 3.664A  pdb=" N   TYR A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
      removed outlier: 5.673A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 5.996A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.542A  pdb=" N   LEU A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   VAL A 376 " --> pdb=" O   GLY A 372 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 422
      removed outlier: 4.155A  pdb=" N   MET A 411 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 427 through 455
      Proline residue:  A 445  - end of helix
    Processing helix  chain 'A' and resid 456 through 472
      removed outlier: 3.692A  pdb=" N   LEU A 460 " --> pdb=" O   GLY A 456 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   MET A 461 " --> pdb=" O   PHE A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 479
      removed outlier: 3.535A  pdb=" N   ARG A 479 " --> pdb=" O   TYR A 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 54
      removed outlier: 3.971A  pdb=" N   VAL B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B  24 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL B  41 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   VAL B  42 " --> pdb=" O   PHE B  38 " (cutoff:3.500A)
      Proline residue:  B  43  - end of helix
      Proline residue:  B  46  - end of helix
      removed outlier: 3.720A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 165
      removed outlier: 4.098A  pdb=" N   GLU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 4.887A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ALA B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER B 145 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 4.933A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
      Proline residue:  B 155  - end of helix
      removed outlier: 4.338A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 166 through 187
      removed outlier: 3.523A  pdb=" N   MET B 170 " --> pdb=" O   TYR B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.861A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 244
      removed outlier: 3.765A  pdb=" N   GLY B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 254
      removed outlier: 3.782A  pdb=" N   GLU B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.593A  pdb=" N   LEU B 261 " --> pdb=" O   SER B 257 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   CYS B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 299 through 318
      removed outlier: 3.511A  pdb=" N   ALA B 305 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 330
    Processing helix  chain 'B' and resid 338 through 341
      removed outlier: 3.505A  pdb=" N   ALA B 341 " --> pdb=" O   LEU B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 341'
    Processing helix  chain 'B' and resid 342 through 360
      removed outlier: 3.835A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
      removed outlier: 3.522A  pdb=" N   CYS B 368 " --> pdb=" O   GLY B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 422
      removed outlier: 4.115A  pdb=" N   MET B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      Proline residue:  B 412  - end of helix
    Processing helix  chain 'B' and resid 427 through 455
      removed outlier: 3.681A  pdb=" N   ILE B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      Proline residue:  B 445  - end of helix
      removed outlier: 3.875A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
      removed outlier: 3.700A  pdb=" N   LEU B 460 " --> pdb=" O   GLY B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479
      removed outlier: 3.634A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 479 " --> pdb=" O   TYR B 476 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.68

  Time building geometry restraints manager: 1.87 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 868
        1.29 -     1.42: 1554
        1.42 -     1.55: 3447
        1.55 -     1.68: 3
        1.68 -     1.81: 102
  Bond restraints: 5974
  Sorted by residual:
  bond pdb=" C   PRO A 481 "
       pdb=" O   PRO A 481 "
    ideal  model  delta    sigma   weight residual
    1.240  1.161  0.080 1.12e-02 7.97e+03 5.06e+01
  bond pdb=" C31 YHR A 601 "
       pdb=" O30 YHR A 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.406 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C31 YHR B 601 "
       pdb=" O30 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.326  1.403 -0.077 2.00e-02 2.50e+03 1.47e+01
  bond pdb=" C17 YHR B 601 "
       pdb=" O19 YHR B 601 "
    ideal  model  delta    sigma   weight residual
    1.325  1.399 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C   PRO B 481 "
       pdb=" O   PRO B 481 "
    ideal  model  delta    sigma   weight residual
    1.240  1.200  0.041 1.12e-02 7.97e+03 1.33e+01
  ... (remaining 5969 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 8048
        3.77 -     7.54: 80
        7.54 -    11.31: 10
       11.31 -    15.07: 0
       15.07 -    18.84: 2
  Bond angle restraints: 8140
  Sorted by residual:
  angle pdb=" C   PRO B 482 "
        pdb=" CA  PRO B 482 "
        pdb=" CB  PRO B 482 "
      ideal   model   delta    sigma   weight residual
     111.46  102.41    9.05 1.29e+00 6.01e-01 4.92e+01
  angle pdb=" N   ARG B 225 "
        pdb=" CA  ARG B 225 "
        pdb=" C   ARG B 225 "
      ideal   model   delta    sigma   weight residual
     111.28  104.37    6.91 1.09e+00 8.42e-01 4.02e+01
  angle pdb=" C7  YHR A 601 "
        pdb=" N8  YHR A 601 "
        pdb=" C9  YHR A 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.73  -18.84 3.00e+00 1.11e-01 3.95e+01
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.67  -18.78 3.00e+00 1.11e-01 3.92e+01
  angle pdb=" C   PRO A 481 "
        pdb=" N   PRO A 482 "
        pdb=" CA  PRO A 482 "
      ideal   model   delta    sigma   weight residual
     120.98  115.56    5.42 1.07e+00 8.73e-01 2.56e+01
  ... (remaining 8135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.89: 3150
       22.89 -    45.78: 333
       45.78 -    68.66: 35
       68.66 -    91.55: 14
       91.55 -   114.44: 2
  Dihedral angle restraints: 3534
    sinusoidal: 1380
      harmonic: 2154
  Sorted by residual:
  dihedral pdb=" C   PRO B 482 "
           pdb=" N   PRO B 482 "
           pdb=" CA  PRO B 482 "
           pdb=" CB  PRO B 482 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -110.63  -10.07     0      2.50e+00 1.60e-01 1.62e+01
  dihedral pdb=" C13 YHR A 601 "
           pdb=" C7  YHR A 601 "
           pdb=" N8  YHR A 601 "
           pdb=" C6  YHR A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -56.78  114.44     1      3.00e+01 1.11e-03 1.51e+01
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -56.10  113.76     1      3.00e+01 1.11e-03 1.50e+01
  ... (remaining 3531 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 874
       0.082 -    0.165: 93
       0.165 -    0.247: 4
       0.247 -    0.329: 1
       0.329 -    0.411: 2
  Chirality restraints: 974
  Sorted by residual:
  chirality pdb=" C13 YHR A 601 "
            pdb=" C12 YHR A 601 "
            pdb=" C14 YHR A 601 "
            pdb=" N8  YHR A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.70    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.69    0.40 2.00e-01 2.50e+01 3.99e+00
  chirality pdb=" CA  PHE A 131 "
            pdb=" N   PHE A 131 "
            pdb=" C   PHE A 131 "
            pdb=" CB  PHE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.93e+00
  ... (remaining 971 not shown)

  Planarity restraints: 988
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 472 "    0.062 5.00e-02 4.00e+02   9.41e-02 1.42e+01
        pdb=" N   PRO B 473 "   -0.163 5.00e-02 4.00e+02
        pdb=" CA  PRO B 473 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO B 473 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 426 "    0.015 2.00e-02 2.50e+03   2.16e-02 9.33e+00
        pdb=" CG  TYR A 426 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 426 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 426 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 426 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 426 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 426 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 426 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  42 "    0.049 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO B  43 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B  43 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  43 "    0.041 5.00e-02 4.00e+02
  ... (remaining 985 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1653
        2.80 -     3.33: 5569
        3.33 -     3.85: 9526
        3.85 -     4.38: 10285
        4.38 -     4.90: 18577
  Nonbonded interactions: 45610
  Sorted by model distance:
  nonbonded pdb=" O   THR B 291 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OE1 GLU A 135 "
            pdb=" NH1 ARG A 138 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   ARG A 365 "
            pdb=" OG  SER A 409 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLY A 158 "
            pdb=" OG1 THR A 161 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" OG1 THR A 291 "
            pdb=" O   THR A 423 "
     model   vdw
     2.347 3.040
  ... (remaining 45605 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.230
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     19.160
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.080   5974  Z= 0.348
  Angle     :  0.973  18.843   8140  Z= 0.523
  Chirality :  0.052   0.411    974
  Planarity :  0.009   0.094    988
  Dihedral  : 17.986 114.441   2166
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.04 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 32.41 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.30), residues: 756
  helix:  1.09 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -1.73 (0.41), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.019   0.002   PHE B 265 
 TYR   0.052   0.002   TYR A 426 
 ARG   0.010   0.001   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14516 (  442)
  hydrogen bonds       : angle       5.39266 ( 1296)
  covalent geometry    : bond        0.00655 ( 5974)
  covalent geometry    : angle       0.97298 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  439 MET cc_start: 0.8235 (tpp) cc_final: 0.7662 (mpp)
REVERT: B  163 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7453 (mtp180)
REVERT: B  229 MET cc_start: 0.7887 (mmm) cc_final: 0.7625 (mmm)
REVERT: B  373 MET cc_start: 0.7738 (mtp) cc_final: 0.7413 (mtp)
REVERT: B  482 PRO cc_start: 0.8860 (Cg_exo) cc_final: 0.8607 (Cg_endo)
  outliers start: 4
  outliers final: 3
  residues processed: 138
  average time/residue: 0.1208
  time to fit residues: 23.9848
Evaluate side-chains
  130 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  163 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 23 optimal weight:    0.4980
   chunk 36 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.4980
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A  35 ASN
A 329 GLN
B  35 ASN
B 329 GLN
B 468 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.110888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.099756 restraints weight = 8113.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.102805 restraints weight = 3846.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.104816 restraints weight = 2211.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5974  Z= 0.157
  Angle     :  0.686   7.552   8140  Z= 0.328
  Chirality :  0.043   0.157    974
  Planarity :  0.006   0.057    988
  Dihedral  :  7.076  54.674    944
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.18 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.31), residues: 756
  helix:  1.80 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.50 (0.45), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 459 
 HIS   0.001   0.000   HIS A 416 
 PHE   0.014   0.001   PHE A 356 
 TYR   0.010   0.001   TYR B 476 
 ARG   0.004   0.001   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05365 (  442)
  hydrogen bonds       : angle       4.21088 ( 1296)
  covalent geometry    : bond        0.00355 ( 5974)
  covalent geometry    : angle       0.68619 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.637 
Fit side-chains
REVERT: A  168 ILE cc_start: 0.8167 (mp) cc_final: 0.7936 (mm)
REVERT: A  174 PHE cc_start: 0.7971 (t80) cc_final: 0.7693 (t80)
REVERT: A  381 LEU cc_start: 0.8167 (mp) cc_final: 0.7758 (mp)
REVERT: B  229 MET cc_start: 0.7602 (mmm) cc_final: 0.7203 (mmm)
REVERT: B  236 LEU cc_start: 0.7681 (mt) cc_final: 0.7465 (mt)
REVERT: B  261 LEU cc_start: 0.7793 (mm) cc_final: 0.7536 (mm)
REVERT: B  373 MET cc_start: 0.7287 (mtp) cc_final: 0.6909 (mtp)
  outliers start: 25
  outliers final: 5
  residues processed: 149
  average time/residue: 0.1323
  time to fit residues: 27.8643
Evaluate side-chains
  137 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   35 ASN
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  240 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0270
   chunk 42 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0070
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.2856

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

Flipped N/Q/H residues before XYZ refinement:
B 361 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.113029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.100704 restraints weight = 8479.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.104007 restraints weight = 3946.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106126 restraints weight = 2248.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5974  Z= 0.134
  Angle     :  0.648   7.064   8140  Z= 0.310
  Chirality :  0.042   0.205    974
  Planarity :  0.005   0.045    988
  Dihedral  :  6.221  51.399    938
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 27.20 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.31), residues: 756
  helix:  1.82 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -2.28 (0.41), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 326 
 HIS   0.001   0.000   HIS A 416 
 PHE   0.018   0.001   PHE A 356 
 TYR   0.009   0.001   TYR B 190 
 ARG   0.003   0.000   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04854 (  442)
  hydrogen bonds       : angle       4.11151 ( 1296)
  covalent geometry    : bond        0.00288 ( 5974)
  covalent geometry    : angle       0.64834 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A  168 ILE cc_start: 0.8147 (mp) cc_final: 0.7922 (mm)
REVERT: A  174 PHE cc_start: 0.7979 (t80) cc_final: 0.7620 (t80)
REVERT: A  245 PRO cc_start: 0.8497 (Cg_endo) cc_final: 0.8291 (Cg_exo)
REVERT: A  296 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8314 (mp)
REVERT: A  381 LEU cc_start: 0.8228 (mp) cc_final: 0.7919 (mp)
REVERT: B  229 MET cc_start: 0.7587 (mmm) cc_final: 0.7379 (mmm)
REVERT: B  261 LEU cc_start: 0.7733 (mm) cc_final: 0.7459 (mm)
REVERT: B  274 GLN cc_start: 0.7527 (pt0) cc_final: 0.7066 (pt0)
REVERT: B  295 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6406 (mpp)
REVERT: B  373 MET cc_start: 0.7310 (mtp) cc_final: 0.6951 (mtp)
  outliers start: 22
  outliers final: 7
  residues processed: 144
  average time/residue: 0.1145
  time to fit residues: 23.7638
Evaluate side-chains
  138 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 52 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   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  35 ASN
A 313 ASN
B 313 ASN
B 361 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.110697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.100004 restraints weight = 8267.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.102922 restraints weight = 3936.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.104828 restraints weight = 2281.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   5974  Z= 0.201
  Angle     :  0.668   6.715   8140  Z= 0.324
  Chirality :  0.046   0.186    974
  Planarity :  0.006   0.048    988
  Dihedral  :  5.899  50.656    938
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 26.38 %
    Favored  : 67.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.31), residues: 756
  helix:  1.80 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.12 (0.42), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 366 
 HIS   0.002   0.000   HIS A 416 
 PHE   0.020   0.001   PHE B 356 
 TYR   0.014   0.001   TYR B 476 
 ARG   0.003   0.000   ARG A 479 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05624 (  442)
  hydrogen bonds       : angle       4.12698 ( 1296)
  covalent geometry    : bond        0.00480 ( 5974)
  covalent geometry    : angle       0.66800 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.611 
Fit side-chains
REVERT: A   43 PRO cc_start: 0.8506 (Cg_endo) cc_final: 0.8277 (Cg_exo)
REVERT: A  149 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6479 (ttm)
REVERT: A  174 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7750 (t80)
REVERT: A  340 LEU cc_start: 0.7782 (mt) cc_final: 0.7404 (mp)
REVERT: A  381 LEU cc_start: 0.8345 (mp) cc_final: 0.8044 (mp)
REVERT: B  261 LEU cc_start: 0.7781 (mm) cc_final: 0.7563 (mm)
REVERT: B  295 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6451 (mpp)
REVERT: B  373 MET cc_start: 0.7242 (mtp) cc_final: 0.6936 (mtp)
REVERT: B  410 MET cc_start: 0.8443 (mmt) cc_final: 0.8206 (tpp)
  outliers start: 36
  outliers final: 15
  residues processed: 158
  average time/residue: 0.1233
  time to fit residues: 27.7365
Evaluate side-chains
  155 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  136 ILE
Chi-restraints excluded: chain B residue  233 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    0.4980
   chunk 36 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 8 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0670
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
A 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.107808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.096944 restraints weight = 8256.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.099687 restraints weight = 4089.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.101518 restraints weight = 2450.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5974  Z= 0.150
  Angle     :  0.639   8.450   8140  Z= 0.307
  Chirality :  0.043   0.143    974
  Planarity :  0.005   0.044    988
  Dihedral  :  5.648  55.346    938
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 27.85 %
    Favored  : 67.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.31), residues: 756
  helix:  1.86 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.07 (0.43), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 
 PHE   0.019   0.001   PHE B 356 
 TYR   0.010   0.001   TYR B 476 
 ARG   0.002   0.000   ARG A 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05061 (  442)
  hydrogen bonds       : angle       4.06863 ( 1296)
  covalent geometry    : bond        0.00340 ( 5974)
  covalent geometry    : angle       0.63886 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 139
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A   43 PRO cc_start: 0.8528 (Cg_endo) cc_final: 0.8316 (Cg_exo)
REVERT: A  174 PHE cc_start: 0.7936 (t80) cc_final: 0.7641 (t80)
REVERT: A  245 PRO cc_start: 0.8474 (Cg_endo) cc_final: 0.8231 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7757 (mt) cc_final: 0.7428 (mp)
REVERT: A  381 LEU cc_start: 0.8344 (mp) cc_final: 0.8018 (mp)
REVERT: B  261 LEU cc_start: 0.7798 (mm) cc_final: 0.7583 (mm)
REVERT: B  295 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6439 (mpp)
REVERT: B  373 MET cc_start: 0.7288 (mtp) cc_final: 0.6930 (mtp)
REVERT: B  410 MET cc_start: 0.8442 (mmt) cc_final: 0.8155 (tpp)
  outliers start: 30
  outliers final: 15
  residues processed: 152
  average time/residue: 0.1164
  time to fit residues: 25.3351
Evaluate side-chains
  151 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 135
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0570
   chunk 58 optimal weight:    0.0980
   chunk 10 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 52 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.3298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.112245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.101062 restraints weight = 8186.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.103968 restraints weight = 4015.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105873 restraints weight = 2377.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.1793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5974  Z= 0.133
  Angle     :  0.628   7.627   8140  Z= 0.302
  Chirality :  0.043   0.172    974
  Planarity :  0.005   0.047    988
  Dihedral  :  5.603  55.789    936
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 28.83 %
    Favored  : 66.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.31), residues: 756
  helix:  1.97 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.09 (0.42), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 387 
 PHE   0.019   0.001   PHE B 356 
 TYR   0.009   0.001   TYR B 190 
 ARG   0.010   0.001   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  442)
  hydrogen bonds       : angle       4.01817 ( 1296)
  covalent geometry    : bond        0.00292 ( 5974)
  covalent geometry    : angle       0.62809 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7652 (t80)
REVERT: A  245 PRO cc_start: 0.8499 (Cg_endo) cc_final: 0.8277 (Cg_exo)
REVERT: A  340 LEU cc_start: 0.7673 (mt) cc_final: 0.7360 (mp)
REVERT: A  371 ILE cc_start: 0.7961 (mm) cc_final: 0.7584 (mt)
REVERT: A  381 LEU cc_start: 0.8301 (mp) cc_final: 0.7975 (mp)
REVERT: A  479 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6710 (ptt-90)
REVERT: B  245 PRO cc_start: 0.8147 (Cg_endo) cc_final: 0.7874 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7738 (mm) cc_final: 0.7523 (mm)
REVERT: B  295 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6459 (mpp)
REVERT: B  373 MET cc_start: 0.7345 (mtp) cc_final: 0.6947 (mtp)
REVERT: B  410 MET cc_start: 0.8410 (mmt) cc_final: 0.8127 (tpp)
REVERT: B  423 THR cc_start: 0.8309 (m) cc_final: 0.7977 (p)
  outliers start: 30
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1229
  time to fit residues: 25.1162
Evaluate side-chains
  151 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 54 optimal weight:    0.2980
   chunk 36 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.2536

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

Flipped N/Q/H residues before XYZ refinement:
A 274 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.104790 restraints weight = 8087.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107821 restraints weight = 3828.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109768 restraints weight = 2194.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5974  Z= 0.125
  Angle     :  0.620   7.138   8140  Z= 0.298
  Chirality :  0.042   0.207    974
  Planarity :  0.005   0.039    988
  Dihedral  :  5.576  54.347    936
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 30.13 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.31), residues: 756
  helix:  2.07 (0.22), residues: 602
  sheet:  None (None), residues: 0
  loop : -2.05 (0.42), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 326 
 HIS   0.001   0.000   HIS A 387 
 PHE   0.015   0.001   PHE A 356 
 TYR   0.009   0.001   TYR B 190 
 ARG   0.006   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04451 (  442)
  hydrogen bonds       : angle       3.99583 ( 1296)
  covalent geometry    : bond        0.00263 ( 5974)
  covalent geometry    : angle       0.61951 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.605 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7881 (OUTLIER) cc_final: 0.7563 (t80)
REVERT: A  340 LEU cc_start: 0.7641 (mt) cc_final: 0.7352 (mp)
REVERT: A  371 ILE cc_start: 0.7986 (mm) cc_final: 0.7594 (mt)
REVERT: A  381 LEU cc_start: 0.8368 (mp) cc_final: 0.8030 (mp)
REVERT: A  439 MET cc_start: 0.7282 (tpp) cc_final: 0.6968 (mpp)
REVERT: A  479 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6728 (ptt-90)
REVERT: B  245 PRO cc_start: 0.8099 (Cg_endo) cc_final: 0.7814 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7726 (mm) cc_final: 0.7502 (mm)
REVERT: B  295 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6469 (mpp)
REVERT: B  370 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7617 (tt)
REVERT: B  373 MET cc_start: 0.7260 (mtp) cc_final: 0.6898 (mtp)
REVERT: B  410 MET cc_start: 0.8435 (mmt) cc_final: 0.8135 (tpp)
REVERT: B  423 THR cc_start: 0.8309 (m) cc_final: 0.8017 (p)
REVERT: B  428 SER cc_start: 0.7840 (p) cc_final: 0.7610 (m)
  outliers start: 27
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1298
  time to fit residues: 27.8037
Evaluate side-chains
  154 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  177 MET
Chi-restraints excluded: chain B residue  180 SER
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 65 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.109795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099183 restraints weight = 8154.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.101966 restraints weight = 4008.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103790 restraints weight = 2390.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5974  Z= 0.147
  Angle     :  0.632   6.705   8140  Z= 0.305
  Chirality :  0.044   0.192    974
  Planarity :  0.006   0.073    988
  Dihedral  :  5.600  54.155    936
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 29.97 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.31), residues: 756
  helix:  2.06 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -1.98 (0.42), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 416 
 PHE   0.014   0.001   PHE A 356 
 TYR   0.011   0.001   TYR B 476 
 ARG   0.006   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  442)
  hydrogen bonds       : angle       3.99071 ( 1296)
  covalent geometry    : bond        0.00338 ( 5974)
  covalent geometry    : angle       0.63216 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7602 (t80)
REVERT: A  340 LEU cc_start: 0.7749 (mt) cc_final: 0.7411 (mp)
REVERT: A  371 ILE cc_start: 0.8029 (mm) cc_final: 0.7620 (mt)
REVERT: A  381 LEU cc_start: 0.8385 (mp) cc_final: 0.8060 (mp)
REVERT: A  479 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.6775 (ptt-90)
REVERT: B  229 MET cc_start: 0.8116 (mmm) cc_final: 0.7750 (mmm)
REVERT: B  245 PRO cc_start: 0.8119 (Cg_endo) cc_final: 0.7830 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: B  295 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6493 (mpp)
REVERT: B  373 MET cc_start: 0.7273 (mtp) cc_final: 0.6915 (mtp)
REVERT: B  410 MET cc_start: 0.8422 (mmt) cc_final: 0.8120 (tpp)
REVERT: B  423 THR cc_start: 0.8336 (m) cc_final: 0.8036 (p)
  outliers start: 28
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1245
  time to fit residues: 25.6540
Evaluate side-chains
  152 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0040
   chunk 45 optimal weight:    0.0060
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.2808

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.112795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.102161 restraints weight = 8087.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.105021 restraints weight = 3970.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.106888 restraints weight = 2345.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5974  Z= 0.125
  Angle     :  0.623   7.858   8140  Z= 0.298
  Chirality :  0.042   0.151    974
  Planarity :  0.006   0.068    988
  Dihedral  :  5.558  55.097    936
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 31.43 %
    Favored  : 64.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.31), residues: 756
  helix:  2.11 (0.22), residues: 604
  sheet:  None (None), residues: 0
  loop : -1.99 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 326 
 HIS   0.001   0.000   HIS A 387 
 PHE   0.016   0.001   PHE B 246 
 TYR   0.009   0.001   TYR B 190 
 ARG   0.005   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04344 (  442)
  hydrogen bonds       : angle       3.96564 ( 1296)
  covalent geometry    : bond        0.00271 ( 5974)
  covalent geometry    : angle       0.62311 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7562 (t80)
REVERT: A  340 LEU cc_start: 0.7680 (mt) cc_final: 0.7339 (mp)
REVERT: A  371 ILE cc_start: 0.7984 (mm) cc_final: 0.7581 (mt)
REVERT: A  381 LEU cc_start: 0.8367 (mp) cc_final: 0.8033 (mp)
REVERT: A  439 MET cc_start: 0.7290 (tpp) cc_final: 0.7025 (mpp)
REVERT: A  479 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6729 (ptt-90)
REVERT: B  229 MET cc_start: 0.7987 (mmm) cc_final: 0.7679 (mmm)
REVERT: B  245 PRO cc_start: 0.8067 (Cg_endo) cc_final: 0.7778 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7552 (mm)
REVERT: B  295 MET cc_start: 0.6765 (OUTLIER) cc_final: 0.6489 (mpp)
REVERT: B  296 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7819 (mp)
REVERT: B  373 MET cc_start: 0.7278 (mtp) cc_final: 0.6869 (mtp)
REVERT: B  410 MET cc_start: 0.8396 (mmt) cc_final: 0.8100 (tpp)
REVERT: B  423 THR cc_start: 0.8309 (m) cc_final: 0.7998 (p)
  outliers start: 24
  outliers final: 17
  residues processed: 139
  average time/residue: 0.1285
  time to fit residues: 25.2108
Evaluate side-chains
  150 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0050
   chunk 24 optimal weight:    0.0570
   chunk 58 optimal weight:    0.0970
   chunk 68 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 60 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.3110

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.104771 restraints weight = 8116.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.107794 restraints weight = 3851.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.109663 restraints weight = 2213.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5974  Z= 0.129
  Angle     :  0.625   7.994   8140  Z= 0.298
  Chirality :  0.042   0.152    974
  Planarity :  0.005   0.064    988
  Dihedral  :  5.570  56.078    936
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 31.76 %
    Favored  : 64.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.32), residues: 756
  helix:  2.13 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -1.85 (0.43), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 366 
 HIS   0.001   0.000   HIS A 387 
 PHE   0.015   0.001   PHE A 356 
 TYR   0.008   0.001   TYR B 476 
 ARG   0.005   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04388 (  442)
  hydrogen bonds       : angle       3.96597 ( 1296)
  covalent geometry    : bond        0.00284 ( 5974)
  covalent geometry    : angle       0.62453 ( 8140)

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

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

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1512 Ramachandran restraints generated.
    756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A  174 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7585 (t80)
REVERT: A  340 LEU cc_start: 0.7676 (mt) cc_final: 0.7345 (mp)
REVERT: A  371 ILE cc_start: 0.7991 (mm) cc_final: 0.7591 (mt)
REVERT: A  381 LEU cc_start: 0.8380 (mp) cc_final: 0.8063 (mp)
REVERT: A  439 MET cc_start: 0.7290 (tpp) cc_final: 0.6992 (mpp)
REVERT: A  479 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6746 (ptt-90)
REVERT: B  229 MET cc_start: 0.7974 (mmm) cc_final: 0.7690 (mmm)
REVERT: B  245 PRO cc_start: 0.8061 (Cg_endo) cc_final: 0.7790 (Cg_exo)
REVERT: B  261 LEU cc_start: 0.7724 (mm) cc_final: 0.7504 (mm)
REVERT: B  295 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6492 (mpp)
REVERT: B  296 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7841 (mp)
REVERT: B  373 MET cc_start: 0.7269 (mtp) cc_final: 0.6903 (mtp)
REVERT: B  410 MET cc_start: 0.8399 (mmt) cc_final: 0.8099 (tpp)
REVERT: B  423 THR cc_start: 0.8314 (m) cc_final: 0.8010 (p)
  outliers start: 23
  outliers final: 17
  residues processed: 140
  average time/residue: 0.1281
  time to fit residues: 25.4429
Evaluate side-chains
  151 residues out of total 614 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue   41 VAL
Chi-restraints excluded: chain A residue   44 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  289 LYS
Chi-restraints excluded: chain A residue  413 ILE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  479 ARG
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  240 LEU
Chi-restraints excluded: chain B residue  295 MET
Chi-restraints excluded: chain B residue  296 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  447 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0070
   chunk 54 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    0.5198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.114025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103263 restraints weight = 8060.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.106221 restraints weight = 3835.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.108150 restraints weight = 2222.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5974  Z= 0.157
  Angle     :  0.647   8.220   8140  Z= 0.310
  Chirality :  0.044   0.186    974
  Planarity :  0.006   0.075    988
  Dihedral  :  5.638  57.597    936
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 31.11 %
    Favored  : 64.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.32), residues: 756
  helix:  2.06 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -1.91 (0.43), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 366 
 HIS   0.003   0.001   HIS B 387 
 PHE   0.015   0.001   PHE A 356 
 TYR   0.012   0.001   TYR B 476 
 ARG   0.005   0.000   ARG A 163 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04870 (  442)
  hydrogen bonds       : angle       4.00279 ( 1296)
  covalent geometry    : bond        0.00367 ( 5974)
  covalent geometry    : angle       0.64724 ( 8140)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2093.52 seconds
wall clock time: 37 minutes 16.53 seconds (2236.53 seconds total)