Starting phenix.real_space_refine
on Tue Mar 11 17:10:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gah_29899/03_2025/8gah_29899.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.079
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: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     Cl      4      4.86       5
     C    4232      2.51       5
     N    1059      2.21       5
     O    1089      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6424
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3205
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 412}
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3215
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 412}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.94, per 1000 atoms: 0.77
  Number of scatterers: 6424
  At special positions: 0
  Unit cell: (80.025, 107.25, 75.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      4     17.00
     S      40     16.00
     O    1089      8.00
     N    1059      7.00
     C    4232      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: 1.77
  Conformation dependent library (CDL) restraints added in 969.3 milliseconds
  

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 1 sheets defined
      76.2% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 46
      removed outlier: 3.561A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 66
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 3.646A  pdb=" N   ALA A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 114
    Processing helix  chain 'A' and resid 123 through 141
      Proline residue:  A 129  - end of helix
      removed outlier: 3.626A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 166
    Processing helix  chain 'A' and resid 170 through 175
      removed outlier: 3.617A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 190
      removed outlier: 4.787A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 5.477A  pdb=" N   ALA A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 203
      removed outlier: 3.765A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 3.925A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 278
      removed outlier: 3.518A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.980A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 283
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.877A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.599A  pdb=" N   SER A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.706A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 349
      removed outlier: 3.525A  pdb=" N   ILE A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 379
      removed outlier: 3.583A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.735A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 393
      removed outlier: 4.000A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 404 through 416
      removed outlier: 3.520A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 440
      removed outlier: 3.637A  pdb=" N   ALA A 432 " --> pdb=" O   THR A 428 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   GLN A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 457
      removed outlier: 3.617A  pdb=" N   ALA A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   LYS A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 65
      removed outlier: 3.904A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 74 through 79
    Processing helix  chain 'B' and resid 79 through 100
      removed outlier: 4.033A  pdb=" N   ALA B  85 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B  89 " --> pdb=" O   ALA B  85 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 3.757A  pdb=" N   GLY B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 126 through 131
      removed outlier: 3.750A  pdb=" N   VAL B 130 " --> pdb=" O   ARG B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 132 through 139
      removed outlier: 3.791A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 165
      removed outlier: 4.025A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 188
      removed outlier: 3.676A  pdb=" N   LEU B 177 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 3.829A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ILE B 201 " --> pdb=" O   ILE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 233
      removed outlier: 4.195A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 252
    Processing helix  chain 'B' and resid 253 through 281
      removed outlier: 3.605A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 287 through 305
      removed outlier: 3.502A  pdb=" N   VAL B 292 " --> pdb=" O   ILE B 288 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   MET B 294 " --> pdb=" O   LYS B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 325
      removed outlier: 3.513A  pdb=" N   ALA B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.755A  pdb=" N   LEU B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 375
      removed outlier: 3.797A  pdb=" N   VAL B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 393
      removed outlier: 4.054A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 397
      removed outlier: 4.130A  pdb=" N   LEU B 397 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 394 through 397'
    Processing helix  chain 'B' and resid 404 through 413
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 428
      removed outlier: 3.609A  pdb=" N   ILE B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 440
      removed outlier: 3.664A  pdb=" N   GLY B 440 " --> pdb=" O   ALA B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.215A  pdb=" N   GLU B 459 " --> pdb=" O   LYS B 455 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLN B 460 " --> pdb=" O   GLN B 456 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211

    401 hydrogen bonds defined for protein.
    1179 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: 1.70

  Time building geometry restraints manager: 2.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1593
        1.33 -     1.45: 1215
        1.45 -     1.57: 3681
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6563
  Sorted by residual:
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.386 -0.052 2.34e-02 1.83e+03 4.91e+00
  bond pdb=" C   ILE B 109 "
       pdb=" N   PRO B 110 "
    ideal  model  delta    sigma   weight residual
    1.334  1.383 -0.049 2.34e-02 1.83e+03 4.40e+00
  bond pdb=" CA  LEU A 136 "
       pdb=" C   LEU A 136 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 1.24e-02 6.50e+03 4.34e+00
  bond pdb=" C   LEU A 136 "
       pdb=" O   LEU A 136 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.022 1.15e-02 7.56e+03 3.52e+00
  bond pdb=" CG  LEU A 145 "
       pdb=" CD1 LEU A 145 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 2.94e+00
  ... (remaining 6558 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 8541
        1.87 -     3.75: 302
        3.75 -     5.62: 55
        5.62 -     7.49: 16
        7.49 -     9.37: 6
  Bond angle restraints: 8920
  Sorted by residual:
  angle pdb=" N   LEU B 163 "
        pdb=" CA  LEU B 163 "
        pdb=" C   LEU B 163 "
      ideal   model   delta    sigma   weight residual
     114.62  106.26    8.36 1.14e+00 7.69e-01 5.38e+01
  angle pdb=" C   GLY A 108 "
        pdb=" N   ILE A 109 "
        pdb=" CA  ILE A 109 "
      ideal   model   delta    sigma   weight residual
     120.24  122.95   -2.71 6.30e-01 2.52e+00 1.85e+01
  angle pdb=" CA  LEU B 163 "
        pdb=" C   LEU B 163 "
        pdb=" N   ASP B 164 "
      ideal   model   delta    sigma   weight residual
     119.71  114.82    4.89 1.17e+00 7.31e-01 1.75e+01
  angle pdb=" C   LEU B 413 "
        pdb=" N   GLU B 414 "
        pdb=" CA  GLU B 414 "
      ideal   model   delta    sigma   weight residual
     126.45  133.09   -6.64 1.77e+00 3.19e-01 1.41e+01
  angle pdb=" C   THR A 251 "
        pdb=" N   LEU A 252 "
        pdb=" CA  LEU A 252 "
      ideal   model   delta    sigma   weight residual
     120.60  125.76   -5.16 1.60e+00 3.91e-01 1.04e+01
  ... (remaining 8915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 3398
       17.38 -    34.76: 323
       34.76 -    52.14: 53
       52.14 -    69.51: 6
       69.51 -    86.89: 3
  Dihedral angle restraints: 3783
    sinusoidal: 1403
      harmonic: 2380
  Sorted by residual:
  dihedral pdb=" CA  VAL B 412 "
           pdb=" C   VAL B 412 "
           pdb=" N   LEU B 413 "
           pdb=" CA  LEU B 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.90   20.10     0      5.00e+00 4.00e-02 1.62e+01
  dihedral pdb=" CA  HIS B 284 "
           pdb=" C   HIS B 284 "
           pdb=" N   GLY B 285 "
           pdb=" CA  GLY B 285 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.76   19.24     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLU B 414 "
           pdb=" C   GLU B 414 "
           pdb=" N   MET B 415 "
           pdb=" CA  MET B 415 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.14   18.86     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 3780 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 875
       0.064 -    0.128: 166
       0.128 -    0.192: 13
       0.192 -    0.256: 1
       0.256 -    0.320: 1
  Chirality restraints: 1056
  Sorted by residual:
  chirality pdb=" CG  LEU B 145 "
            pdb=" CB  LEU B 145 "
            pdb=" CD1 LEU B 145 "
            pdb=" CD2 LEU B 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.57e+00
  chirality pdb=" CB  THR A  71 "
            pdb=" CA  THR A  71 "
            pdb=" OG1 THR A  71 "
            pdb=" CG2 THR A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.30e-01
  chirality pdb=" CB  VAL B 341 "
            pdb=" CA  VAL B 341 "
            pdb=" CG1 VAL B 341 "
            pdb=" CG2 VAL B 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.14e-01
  ... (remaining 1053 not shown)

  Planarity restraints: 1116
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO B 359 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO B 267 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.044 5.00e-02 4.00e+02   6.59e-02 6.96e+00
        pdb=" N   PRO A 150 "   -0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1113 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1865
        2.80 -     3.33: 5669
        3.33 -     3.85: 10983
        3.85 -     4.38: 13981
        4.38 -     4.90: 22990
  Nonbonded interactions: 55488
  Sorted by model distance:
  nonbonded pdb=" O   THR B 176 "
            pdb=" OG1 THR B 180 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   THR B 365 "
            pdb=" OG1 THR B 369 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER B  86 "
            pdb=" O   GLY B 141 "
     model   vdw
     2.309 3.040
  ... (remaining 55483 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 30 through 206 or (resid 207 through 208 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 209 through 461 or resid 501 th \ 
rough 502))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.460
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
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      :  0.005   0.065   6563  Z= 0.333
  Angle     :  0.876   9.368   8920  Z= 0.472
  Chirality :  0.049   0.320   1056
  Planarity :  0.008   0.067   1116
  Dihedral  : 13.563  86.891   2283
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  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: -6.49 (0.16), residues: 860
  helix: -4.45 (0.08), residues: 632
  sheet:  None (None), residues: 0
  loop : -2.92 (0.35), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP B 291 
 HIS   0.002   0.001   HIS A 281 
 PHE   0.014   0.001   PHE A 357 
 TYR   0.014   0.002   TYR B 100 
 ARG   0.003   0.000   ARG A 147 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.629 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.7982 (mttt) cc_final: 0.7266 (pttp)
REVERT: A  410 ILE cc_start: 0.8513 (tp) cc_final: 0.8115 (mp)
REVERT: A  455 LYS cc_start: 0.7731 (tttt) cc_final: 0.7079 (ttpt)
REVERT: B   62 ASN cc_start: 0.7062 (m110) cc_final: 0.6861 (t0)
REVERT: B  117 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7700 (mt-10)
REVERT: B  282 ARG cc_start: 0.7810 (mtm110) cc_final: 0.7404 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 1.0806
  time to fit residues: 147.3221
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0770
   chunk 34 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0980
   chunk 50 optimal weight:    0.3980
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 157 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.155668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.132980 restraints weight = 6814.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 1.45
r_work: 0.3435 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3316 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6563  Z= 0.195
  Angle     :  0.618   6.774   8920  Z= 0.319
  Chirality :  0.039   0.131   1056
  Planarity :  0.006   0.048   1116
  Dihedral  :  5.473  26.207    912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.84 %
    Favored  : 85.51 %
  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: -3.25 (0.25), residues: 860
  helix: -1.93 (0.18), residues: 626
  sheet:  None (None), residues: 0
  loop : -2.26 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 291 
 HIS   0.002   0.001   HIS B 284 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.010   0.001   TYR B 100 
 ARG   0.003   0.000   ARG B 126 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.655 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.7704 (mttt) cc_final: 0.6503 (pttp)
REVERT: A  410 ILE cc_start: 0.8102 (tp) cc_final: 0.7691 (mp)
REVERT: A  455 LYS cc_start: 0.7545 (tttt) cc_final: 0.6462 (ttpt)
REVERT: B  119 GLN cc_start: 0.7884 (mt0) cc_final: 0.7292 (mm110)
REVERT: B  166 PHE cc_start: 0.7207 (m-10) cc_final: 0.6804 (m-10)
  outliers start: 17
  outliers final: 6
  residues processed: 126
  average time/residue: 1.0107
  time to fit residues: 134.8720
Evaluate side-chains
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  162 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    0.1980
   chunk 34 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 55 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.152561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.129815 restraints weight = 6973.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.47
r_work: 0.3337 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.213
  Angle     :  0.584   6.553   8920  Z= 0.297
  Chirality :  0.040   0.141   1056
  Planarity :  0.005   0.046   1116
  Dihedral  :  5.237  26.020    912
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.95 %
    Favored  : 82.55 %
  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 (0.28), residues: 860
  helix: -0.56 (0.21), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.03 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 
 PHE   0.012   0.001   PHE A 219 
 TYR   0.010   0.001   TYR B 100 
 ARG   0.006   0.000   ARG A 174 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.7647 (mttt) cc_final: 0.6399 (pttm)
REVERT: A  410 ILE cc_start: 0.8086 (tp) cc_final: 0.7685 (mp)
REVERT: A  455 LYS cc_start: 0.7558 (tttt) cc_final: 0.6422 (ttpt)
REVERT: B  119 GLN cc_start: 0.7896 (mt0) cc_final: 0.7272 (mm110)
REVERT: B  166 PHE cc_start: 0.7231 (m-10) cc_final: 0.6831 (m-10)
REVERT: B  377 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7946 (pt0)
  outliers start: 16
  outliers final: 3
  residues processed: 107
  average time/residue: 1.1300
  time to fit residues: 127.7961
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 52 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 57 optimal weight:    0.1980
   chunk 66 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.151201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.128385 restraints weight = 6931.209|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 1.45
r_work: 0.3331 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6563  Z= 0.237
  Angle     :  0.591   6.816   8920  Z= 0.298
  Chirality :  0.041   0.145   1056
  Planarity :  0.005   0.045   1116
  Dihedral  :  5.175  25.379    912
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.36 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.29), residues: 860
  helix: -0.07 (0.21), residues: 624
  sheet:  None (None), residues: 0
  loop : -1.98 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 291 
 HIS   0.003   0.000   HIS B 284 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.009   0.001   TYR B 100 
 ARG   0.004   0.000   ARG B 147 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6581 (mtt90)
REVERT: A  410 ILE cc_start: 0.8111 (tp) cc_final: 0.7739 (mp)
REVERT: A  455 LYS cc_start: 0.7491 (tttt) cc_final: 0.6370 (ttpt)
REVERT: B  119 GLN cc_start: 0.7958 (mt0) cc_final: 0.7321 (mm110)
REVERT: B  126 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8074 (mtt180)
REVERT: B  166 PHE cc_start: 0.7269 (m-10) cc_final: 0.6838 (m-10)
REVERT: B  317 PHE cc_start: 0.8533 (m-10) cc_final: 0.8300 (m-80)
REVERT: B  377 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7926 (pt0)
  outliers start: 17
  outliers final: 9
  residues processed: 110
  average time/residue: 1.0444
  time to fit residues: 121.8888
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ARG
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  377 GLU
Chi-restraints excluded: chain B residue  398 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 51 optimal weight:    0.1980
   chunk 20 optimal weight:    0.0870
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 0 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.1558

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.156380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.133892 restraints weight = 6854.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3555 rms_B_bonded: 1.45
r_work: 0.3455 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3334 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6563  Z= 0.141
  Angle     :  0.533   6.473   8920  Z= 0.270
  Chirality :  0.038   0.127   1056
  Planarity :  0.004   0.043   1116
  Dihedral  :  4.908  28.592    912
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.54 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.30), residues: 860
  helix:  0.45 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.76 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP A  59 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.006   0.001   TYR A 229 
 ARG   0.003   0.000   ARG B 147 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 ASN cc_start: 0.8665 (m110) cc_final: 0.8402 (m-40)
REVERT: A  174 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7362 (mtp-110)
REVERT: A  271 LYS cc_start: 0.8117 (mttt) cc_final: 0.7006 (mmtt)
REVERT: A  455 LYS cc_start: 0.7519 (tttt) cc_final: 0.6456 (ttpt)
REVERT: B  119 GLN cc_start: 0.7892 (mt0) cc_final: 0.7296 (mm110)
REVERT: B  126 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.8076 (mtt180)
REVERT: B  166 PHE cc_start: 0.7219 (m-10) cc_final: 0.6786 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 109
  average time/residue: 1.0730
  time to fit residues: 123.6772
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  162 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3690 r_free = 0.3690 target = 0.151646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.128795 restraints weight = 6800.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.45
r_work: 0.3312 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6563  Z= 0.259
  Angle     :  0.597   6.807   8920  Z= 0.300
  Chirality :  0.042   0.150   1056
  Planarity :  0.004   0.045   1116
  Dihedral  :  5.056  24.277    912
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.69 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.30), residues: 860
  helix:  0.42 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -1.77 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 291 
 HIS   0.002   0.000   HIS A 175 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.009   0.001   TYR A 255 
 ARG   0.002   0.000   ARG A 174 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.669 
Fit side-chains
REVERT: A  403 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7018 (mtt90)
REVERT: A  455 LYS cc_start: 0.7445 (tttt) cc_final: 0.6333 (ttpt)
REVERT: B   62 ASN cc_start: 0.6972 (m110) cc_final: 0.6709 (t0)
REVERT: B  119 GLN cc_start: 0.7964 (mt0) cc_final: 0.7311 (mm110)
REVERT: B  126 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.8068 (mtt180)
REVERT: B  166 PHE cc_start: 0.7358 (m-10) cc_final: 0.6897 (m-10)
REVERT: B  377 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7915 (pt0)
  outliers start: 20
  outliers final: 7
  residues processed: 116
  average time/residue: 1.0333
  time to fit residues: 126.9156
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 67 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0040
   chunk 10 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 233 ASN
B 191 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.152785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.130163 restraints weight = 6798.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 1.45
r_work: 0.3328 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3207 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6563  Z= 0.209
  Angle     :  0.580   6.780   8920  Z= 0.290
  Chirality :  0.040   0.139   1056
  Planarity :  0.004   0.046   1116
  Dihedral  :  4.996  26.106    912
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.25 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.30), residues: 860
  helix:  0.50 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -1.87 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  59 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.010   0.001   PHE A 219 
 TYR   0.008   0.001   TYR B 100 
 ARG   0.002   0.000   ARG A 174 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.659 
Fit side-chains
REVERT: A  157 ASN cc_start: 0.8761 (m110) cc_final: 0.8555 (m-40)
REVERT: A  290 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7570 (mtmt)
REVERT: A  403 ARG cc_start: 0.7283 (OUTLIER) cc_final: 0.6971 (mtt90)
REVERT: A  410 ILE cc_start: 0.8097 (tp) cc_final: 0.7702 (mp)
REVERT: A  455 LYS cc_start: 0.7367 (tttt) cc_final: 0.6257 (ttpt)
REVERT: B  119 GLN cc_start: 0.7941 (mt0) cc_final: 0.7315 (mm110)
REVERT: B  166 PHE cc_start: 0.7344 (m-10) cc_final: 0.6884 (m-10)
REVERT: B  377 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7908 (pt0)
  outliers start: 17
  outliers final: 8
  residues processed: 107
  average time/residue: 1.0091
  time to fit residues: 114.4861
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  433 THR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0370
   chunk 11 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.3258

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.154627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.132060 restraints weight = 6784.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.45
r_work: 0.3364 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3244 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.2797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6563  Z= 0.171
  Angle     :  0.556   8.485   8920  Z= 0.278
  Chirality :  0.039   0.141   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.881  27.228    912
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 20.09 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.30), residues: 860
  helix:  0.72 (0.22), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.71 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  59 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.009   0.001   PHE A 219 
 TYR   0.007   0.001   TYR B 100 
 ARG   0.002   0.000   ARG B 126 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  157 ASN cc_start: 0.8733 (m110) cc_final: 0.8519 (m-40)
REVERT: A  271 LYS cc_start: 0.8070 (mttt) cc_final: 0.6900 (mmtt)
REVERT: A  290 LYS cc_start: 0.7819 (mtmt) cc_final: 0.7536 (mtmt)
REVERT: A  403 ARG cc_start: 0.7194 (mtm110) cc_final: 0.6966 (mtm-85)
REVERT: A  410 ILE cc_start: 0.8113 (tp) cc_final: 0.7709 (mp)
REVERT: A  455 LYS cc_start: 0.7418 (tttt) cc_final: 0.6322 (ttpt)
REVERT: B  119 GLN cc_start: 0.7909 (mt0) cc_final: 0.7298 (mm110)
REVERT: B  166 PHE cc_start: 0.7309 (m-10) cc_final: 0.6761 (m-10)
REVERT: B  377 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7885 (pt0)
  outliers start: 16
  outliers final: 7
  residues processed: 107
  average time/residue: 0.9774
  time to fit residues: 111.2652
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0980
   chunk 84 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.7980
   chunk 52 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0270
   overall best weight:    0.4038

-------------------------------------------------------------------------------
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 = 0.3719 r_free = 0.3719 target = 0.154178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.131531 restraints weight = 6832.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.46
r_work: 0.3370 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6563  Z= 0.191
  Angle     :  0.574   7.625   8920  Z= 0.285
  Chirality :  0.040   0.193   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.882  25.889    912
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 21.18 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.30), residues: 860
  helix:  0.74 (0.22), residues: 618
  sheet:  None (None), residues: 0
  loop : -1.69 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  59 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.011   0.001   PHE A 219 
 TYR   0.007   0.001   TYR B 100 
 ARG   0.002   0.000   ARG A 167 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.707 
Fit side-chains
REVERT: A  157 ASN cc_start: 0.8770 (m110) cc_final: 0.8526 (m-40)
REVERT: A  271 LYS cc_start: 0.8077 (mttt) cc_final: 0.6896 (mmtt)
REVERT: A  290 LYS cc_start: 0.7811 (mtmt) cc_final: 0.7544 (mtmt)
REVERT: A  403 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6924 (mtt90)
REVERT: A  410 ILE cc_start: 0.8096 (tp) cc_final: 0.7694 (mp)
REVERT: A  455 LYS cc_start: 0.7439 (tttt) cc_final: 0.6341 (ttpt)
REVERT: B  119 GLN cc_start: 0.7910 (mt0) cc_final: 0.7287 (mm110)
REVERT: B  166 PHE cc_start: 0.7318 (m-10) cc_final: 0.6784 (m-10)
REVERT: B  377 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7886 (pt0)
  outliers start: 11
  outliers final: 8
  residues processed: 99
  average time/residue: 1.0606
  time to fit residues: 111.3506
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.152484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.129621 restraints weight = 6826.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3411 rms_B_bonded: 1.46
r_work: 0.3316 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6563  Z= 0.235
  Angle     :  0.603   8.090   8920  Z= 0.299
  Chirality :  0.042   0.212   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.966  24.904    912
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 21.50 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.30), residues: 860
  helix:  0.62 (0.22), residues: 624
  sheet:  None (None), residues: 0
  loop : -1.93 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 291 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.011   0.001   PHE A 219 
 TYR   0.007   0.001   TYR A  94 
 ARG   0.002   0.000   ARG A 167 

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

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

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1720 Ramachandran restraints generated.
    860 Oldfield, 0 Emsley, 860 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  271 LYS cc_start: 0.8120 (mttt) cc_final: 0.6940 (mmtt)
REVERT: A  282 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7625 (mtm-85)
REVERT: A  290 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7617 (mtmt)
REVERT: A  403 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6977 (mtt90)
REVERT: A  410 ILE cc_start: 0.8130 (tp) cc_final: 0.7738 (mp)
REVERT: A  455 LYS cc_start: 0.7450 (tttt) cc_final: 0.6357 (ttpt)
REVERT: B   62 ASN cc_start: 0.7022 (m110) cc_final: 0.6731 (t0)
REVERT: B  119 GLN cc_start: 0.7941 (mt0) cc_final: 0.7316 (mm110)
REVERT: B  166 PHE cc_start: 0.7318 (m-10) cc_final: 0.6827 (m-10)
REVERT: B  377 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7898 (pt0)
  outliers start: 12
  outliers final: 9
  residues processed: 101
  average time/residue: 1.0459
  time to fit residues: 112.0595
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  403 ARG
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain A residue  442 LYS
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  377 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   chunk 39 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.5578

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.152622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.129786 restraints weight = 6940.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3420 rms_B_bonded: 1.47
r_work: 0.3323 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3201 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6563  Z= 0.225
  Angle     :  0.601   8.615   8920  Z= 0.298
  Chirality :  0.042   0.200   1056
  Planarity :  0.004   0.047   1116
  Dihedral  :  4.985  25.198    912
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 21.50 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.30), residues: 860
  helix:  0.62 (0.22), residues: 624
  sheet:  None (None), residues: 0
  loop : -1.91 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  59 
 HIS   0.001   0.000   HIS A 175 
 PHE   0.011   0.001   PHE A 219 
 TYR   0.007   0.001   TYR A  94 
 ARG   0.002   0.000   ARG A 174 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4292.20 seconds
wall clock time: 73 minutes 53.49 seconds (4433.49 seconds total)