Starting phenix.real_space_refine
on Tue Mar  3 18:46:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zt6_14955/03_2026/7zt6_14955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zt6_14955/03_2026/7zt6_14955.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/7zt6_14955/03_2026/7zt6_14955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zt6_14955/03_2026/7zt6_14955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zt6_14955/03_2026/7zt6_14955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zt6_14955/03_2026/7zt6_14955.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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
     P       6      5.49       5
     S      38      5.16       5
     C    5175      2.51       5
     N    1363      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8073
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 3863
          Classifications: {'peptide': 501}
          Incomplete info: {'truncation_to_alanine': 50}
          Link IDs: {'PTRANS': 27, 'TRANS': 473}
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 225
          Unresolved non-hydrogen dihedrals: 145
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 4, 'ASP:plan': 10, 'ARG:plan': 6, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 130
    Chain: "B"
      Number of atoms: 4174
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 530, 4174
          Classifications: {'peptide': 530}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 26, 'TRANS': 503}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 36
          Unusual residues: {'IHP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.03, per 1000 atoms: 0.25
  Number of scatterers: 8073
  At special positions: 0
  Unit cell: (88.02, 92.584, 132.356, 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)
     S      38     16.00
     P       6     15.00
     O    1491      8.00
     N    1363      7.00
     C    5175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 312.3 milliseconds
  

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1970

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      36.9% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.574A  pdb=" N   PHE A  49 " --> pdb=" O   SER A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 78
    Processing helix  chain 'A' and resid 112 through 121
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 179 through 197
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 4.117A  pdb=" N   ASP A 219 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 251
      removed outlier: 3.755A  pdb=" N   THR A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 314
      No H-bonds generated for 'chain 'A' and resid 312 through 314'
    Processing helix  chain 'A' and resid 330 through 338
      removed outlier: 4.044A  pdb=" N   LYS A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 393
      removed outlier: 3.598A  pdb=" N   LEU A 381 " --> pdb=" O   GLY A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 468
    Processing helix  chain 'A' and resid 480 through 496
    Processing helix  chain 'A' and resid 510 through 519
    Processing helix  chain 'A' and resid 520 through 530
    Processing helix  chain 'B' and resid 29 through 48
    Processing helix  chain 'B' and resid 87 through 96
    Processing helix  chain 'B' and resid 106 through 122
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'B' and resid 199 through 217
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.883A  pdb=" N   LEU B 221 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
      removed outlier: 3.982A  pdb=" N   ARG B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 233 through 238
      removed outlier: 4.872A  pdb=" N   VAL B 236 " --> pdb=" O   LYS B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 308
      No H-bonds generated for 'chain 'B' and resid 306 through 308'
    Processing helix  chain 'B' and resid 324 through 332
    Processing helix  chain 'B' and resid 352 through 356
    Processing helix  chain 'B' and resid 370 through 388
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 447 through 461
    Processing helix  chain 'B' and resid 484 through 500
      removed outlier: 3.981A  pdb=" N   GLN B 488 " --> pdb=" O   ASN B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 509 through 516
      removed outlier: 3.600A  pdb=" N   TRP B 513 " --> pdb=" O   GLN B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 537
      removed outlier: 3.911A  pdb=" N   THR B 523 " --> pdb=" O   PRO B 519 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ILE B 528 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      Proline residue:  B 529  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 104
      removed outlier: 6.308A  pdb=" N   SER A  37 " --> pdb=" O   ARG A 165 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   MET A 167 " --> pdb=" O   SER A  37 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ILE A  39 " --> pdb=" O   MET A 167 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   PHE A 169 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU A  41 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   ILE A 166 " --> pdb=" O   ASP A 201 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   MET A 203 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   LEU A 168 " --> pdb=" O   MET A 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262
      removed outlier: 3.536A  pdb=" N   TYR A 369 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TYR A 409 " --> pdb=" O   TYR A 400 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   VAL A 394 " --> pdb=" O   PRO A 415 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   GLY A 349 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ARG A 399 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   LEU A 347 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 289
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 329
    Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 376
      removed outlier: 3.708A  pdb=" N   ILE B 540 " --> pdb=" O   ILE A 376 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 419 through 420
    Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 84
      removed outlier: 6.272A  pdb=" N   HIS B  80 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   LEU B  58 " --> pdb=" O   HIS B  80 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   HIS B  82 " --> pdb=" O   LEU B  56 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   LEU B  56 " --> pdb=" O   HIS B  82 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLU B  53 " --> pdb=" O   ALA B   8 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL B  10 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   ALA B   9 " --> pdb=" O   HIS B 131 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   GLU B 133 " --> pdb=" O   ALA B   9 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   VAL B  11 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   PHE B 135 " --> pdb=" O   VAL B  11 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   CYS B  13 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   ARG B 130 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 8.686A  pdb=" N   GLN B 162 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ILE B 132 " --> pdb=" O   GLN B 162 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   PHE B 164 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   ILE B 134 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 249 through 253
      removed outlier: 3.587A  pdb=" N   LEU B 257 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   VAL B 361 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   ALA B 366 " --> pdb=" O   GLU B 417 " (cutoff:3.500A)
      removed outlier: 9.880A  pdb=" N   GLU B 417 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   VAL B 405 " --> pdb=" O   LEU B 424 " (cutoff:3.500A)
      removed outlier: 8.752A  pdb=" N   MET B 389 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL B 390 " --> pdb=" O   PHE B 345 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B 390 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   ILE B 392 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 467
      removed outlier: 4.481A  pdb=" N   THR B 472 " --> pdb=" O   ASP B 467 " (cutoff:3.500A)

    349 hydrogen bonds defined for protein.
    984 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: 1.38

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2576
        1.34 -     1.46: 1274
        1.46 -     1.57: 4319
        1.57 -     1.69: 6
        1.69 -     1.81: 64
  Bond restraints: 8239
  Sorted by residual:
  bond pdb=" O12 IHP A 701 "
       pdb=" P2  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.675  1.595  0.080 2.00e-02 2.50e+03 1.62e+01
  bond pdb=" O15 IHP A 701 "
       pdb=" P5  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.675  1.598  0.077 2.00e-02 2.50e+03 1.49e+01
  bond pdb=" O16 IHP A 701 "
       pdb=" P6  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.672  1.603  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" C   MET A 446 "
       pdb=" N   PRO A 447 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 1.11e-02 8.12e+03 1.11e+01
  bond pdb=" N   ARG A 444 "
       pdb=" CA  ARG A 444 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.036 1.18e-02 7.18e+03 9.56e+00
  ... (remaining 8234 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 10808
        1.73 -     3.45: 276
        3.45 -     5.18: 46
        5.18 -     6.91: 14
        6.91 -     8.64: 5
  Bond angle restraints: 11149
  Sorted by residual:
  angle pdb=" N   LYS A 358 "
        pdb=" CA  LYS A 358 "
        pdb=" C   LYS A 358 "
      ideal   model   delta    sigma   weight residual
     113.41  108.08    5.33 1.22e+00 6.72e-01 1.91e+01
  angle pdb=" N   VAL B  16 "
        pdb=" CA  VAL B  16 "
        pdb=" C   VAL B  16 "
      ideal   model   delta    sigma   weight residual
     111.88  107.28    4.60 1.06e+00 8.90e-01 1.89e+01
  angle pdb=" N   LYS B 481 "
        pdb=" CA  LYS B 481 "
        pdb=" C   LYS B 481 "
      ideal   model   delta    sigma   weight residual
     113.23  108.09    5.14 1.24e+00 6.50e-01 1.72e+01
  angle pdb=" CA  ILE B 482 "
        pdb=" C   ILE B 482 "
        pdb=" O   ILE B 482 "
      ideal   model   delta    sigma   weight residual
     119.71  115.91    3.80 9.30e-01 1.16e+00 1.67e+01
  angle pdb=" CA  ILE B 482 "
        pdb=" C   ILE B 482 "
        pdb=" N   PRO B 483 "
      ideal   model   delta    sigma   weight residual
     119.15  123.56   -4.41 1.20e+00 6.94e-01 1.35e+01
  ... (remaining 11144 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4641
       17.56 -    35.12: 352
       35.12 -    52.69: 61
       52.69 -    70.25: 16
       70.25 -    87.81: 6
  Dihedral angle restraints: 5076
    sinusoidal: 2051
      harmonic: 3025
  Sorted by residual:
  dihedral pdb=" CA  GLU B 199 "
           pdb=" C   GLU B 199 "
           pdb=" N   GLN B 200 "
           pdb=" CA  GLN B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  MET B  14 "
           pdb=" C   MET B  14 "
           pdb=" N   ASP B  15 "
           pdb=" CA  ASP B  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.08   18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  LYS A 510 "
           pdb=" C   LYS A 510 "
           pdb=" N   VAL A 511 "
           pdb=" CA  VAL A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.34  -18.66     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 1126
       0.074 -    0.148: 134
       0.148 -    0.222: 5
       0.222 -    0.295: 1
       0.295 -    0.369: 1
  Chirality restraints: 1267
  Sorted by residual:
  chirality pdb=" C1  IHP A 701 "
            pdb=" C2  IHP A 701 "
            pdb=" C6  IHP A 701 "
            pdb=" O11 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.32    2.69   -0.37 2.00e-01 2.50e+01 3.41e+00
  chirality pdb=" C5  IHP A 701 "
            pdb=" C4  IHP A 701 "
            pdb=" C6  IHP A 701 "
            pdb=" O15 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -2.66    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" C3  IHP A 701 "
            pdb=" C2  IHP A 701 "
            pdb=" C4  IHP A 701 "
            pdb=" O13 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34   -2.55    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1264 not shown)

  Planarity restraints: 1424
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  71 "    0.014 2.00e-02 2.50e+03   1.12e-02 2.52e+00
        pdb=" CG  TYR A  71 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  71 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  71 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  71 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  71 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  71 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 161 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" C   MET A 161 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   MET A 161 "    0.008 2.00e-02 2.50e+03
        pdb=" N   SER A 162 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 199 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   GLU B 199 "    0.020 2.00e-02 2.50e+03
        pdb=" O   GLU B 199 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLN B 200 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1421 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 970
        2.74 -     3.28: 8723
        3.28 -     3.82: 13693
        3.82 -     4.36: 15737
        4.36 -     4.90: 26381
  Nonbonded interactions: 65504
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 467 "
            pdb=" OG1 THR B 472 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ASP B 116 "
            pdb=" ND1 HIS B 120 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" OG  SER B 348 "
            pdb=" OD2 ASP B 388 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OE2 GLU A 371 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" OH  TYR A 361 "
            pdb=" O   GLY B 358 "
     model   vdw
     2.236 3.040
  ... (remaining 65499 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             2.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.850
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8808
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      :  0.006   0.080   8239  Z= 0.308
  Angle     :  0.707   8.637  11149  Z= 0.389
  Chirality :  0.045   0.369   1267
  Planarity :  0.003   0.027   1424
  Dihedral  : 13.206  87.810   3106
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.35 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.27), residues: 1025
  helix:  1.84 (0.29), residues: 328
  sheet: -0.65 (0.39), residues: 167
  loop : -0.55 (0.28), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.028   0.002   TYR A  71 
 PHE   0.015   0.001   PHE B 135 
 TRP   0.011   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 ( 8239)
  covalent geometry    : angle       0.70655 (11149)
  hydrogen bonds       : bond        0.17604 (  349)
  hydrogen bonds       : angle       7.36730 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   48 MET cc_start: 0.9190 (mmt) cc_final: 0.8882 (mmm)
REVERT: A   62 MET cc_start: 0.9366 (mmp) cc_final: 0.9099 (mmm)
REVERT: A  348 MET cc_start: 0.8698 (mpp) cc_final: 0.8204 (mpp)
REVERT: A  514 MET cc_start: 0.9723 (ptp) cc_final: 0.9435 (pmm)
REVERT: B   13 CYS cc_start: 0.9172 (t) cc_final: 0.8795 (t)
REVERT: B   14 MET cc_start: 0.9160 (tpp) cc_final: 0.8933 (tpp)
REVERT: B  115 MET cc_start: 0.7604 (ppp) cc_final: 0.7173 (ppp)
REVERT: B  479 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8860 (t)
  outliers start: 6
  outliers final: 1
  residues processed: 46
  average time/residue: 0.0845
  time to fit residues: 5.8349
Evaluate side-chains
  35 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 33
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain B residue  479 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.034305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.024351 restraints weight = 59116.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.025271 restraints weight = 31019.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.025923 restraints weight = 20981.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.026326 restraints weight = 16193.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.026631 restraints weight = 13795.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8239  Z= 0.121
  Angle     :  0.562   6.789  11149  Z= 0.283
  Chirality :  0.042   0.142   1267
  Planarity :  0.003   0.033   1424
  Dihedral  :  4.999  51.621   1143
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  5.58 %
    Favored  : 93.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.27), residues: 1025
  helix:  1.98 (0.28), residues: 339
  sheet: -0.14 (0.39), residues: 174
  loop : -0.51 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.016   0.001   TYR A  71 
 PHE   0.011   0.001   PHE B 135 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8239)
  covalent geometry    : angle       0.56218 (11149)
  hydrogen bonds       : bond        0.03800 (  349)
  hydrogen bonds       : angle       5.75653 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  167 MET cc_start: 0.9381 (OUTLIER) cc_final: 0.9126 (mtt)
REVERT: A  346 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8457 (ptp)
REVERT: A  348 MET cc_start: 0.8648 (mpp) cc_final: 0.8345 (mpp)
REVERT: A  398 CYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8624 (t)
REVERT: B   13 CYS cc_start: 0.9331 (t) cc_final: 0.9124 (t)
REVERT: B  115 MET cc_start: 0.7900 (ppp) cc_final: 0.7505 (ppp)
REVERT: B  479 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9097 (t)
  outliers start: 5
  outliers final: 1
  residues processed: 40
  average time/residue: 0.0667
  time to fit residues: 4.4583
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 MET
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  398 CYS
Chi-restraints excluded: chain B residue  479 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 39 optimal weight:    6.9990
   chunk 75 optimal weight:    0.4980
   chunk 96 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0980
   chunk 4 optimal weight:    9.9990
   chunk 9 optimal weight:    7.9990
   chunk 86 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 100 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   overall best weight:    2.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.033992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.024208 restraints weight = 58442.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.025133 restraints weight = 30697.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.025770 restraints weight = 20615.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026207 restraints weight = 15927.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.026497 restraints weight = 13431.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8239  Z= 0.145
  Angle     :  0.538   8.630  11149  Z= 0.270
  Chirality :  0.040   0.137   1267
  Planarity :  0.003   0.024   1424
  Dihedral  :  4.701  45.112   1143
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  8.49 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.27), residues: 1025
  helix:  2.09 (0.28), residues: 339
  sheet: -0.10 (0.40), residues: 174
  loop : -0.45 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.012   0.001   TYR A  71 
 PHE   0.006   0.001   PHE A 432 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8239)
  covalent geometry    : angle       0.53767 (11149)
  hydrogen bonds       : bond        0.03389 (  349)
  hydrogen bonds       : angle       5.48074 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9268 (mmm) cc_final: 0.8960 (mmm)
REVERT: A  203 MET cc_start: 0.9512 (mmm) cc_final: 0.8751 (mmm)
REVERT: A  346 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8275 (ptp)
REVERT: A  348 MET cc_start: 0.8621 (mpp) cc_final: 0.8172 (mpp)
REVERT: A  398 CYS cc_start: 0.8977 (m) cc_final: 0.8573 (t)
REVERT: B  115 MET cc_start: 0.7958 (ppp) cc_final: 0.7468 (ppp)
REVERT: B  212 MET cc_start: 0.9356 (tpp) cc_final: 0.9135 (tpp)
REVERT: B  357 MET cc_start: 0.8938 (mmm) cc_final: 0.8505 (tpp)
REVERT: B  427 MET cc_start: 0.8305 (mpp) cc_final: 0.8101 (mpp)
REVERT: B  479 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9185 (t)
  outliers start: 7
  outliers final: 2
  residues processed: 40
  average time/residue: 0.0670
  time to fit residues: 4.4285
Evaluate side-chains
  37 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  479 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 45 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 3 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 81 optimal weight:    4.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3031 r_free = 0.3031 target = 0.034549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.024946 restraints weight = 60059.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.025866 restraints weight = 30740.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.026488 restraints weight = 20337.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.026882 restraints weight = 15562.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.027195 restraints weight = 13191.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.2642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.1392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8239  Z= 0.194
  Angle     :  0.542   6.922  11149  Z= 0.275
  Chirality :  0.039   0.133   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.554  36.373   1143
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.88 %
    Favored  : 89.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.27), residues: 1025
  helix:  2.03 (0.28), residues: 347
  sheet: -0.18 (0.41), residues: 164
  loop : -0.44 (0.29), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 497 
 TYR   0.011   0.001   TYR A  71 
 PHE   0.009   0.001   PHE B  59 
 TRP   0.010   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B 414 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8239)
  covalent geometry    : angle       0.54206 (11149)
  hydrogen bonds       : bond        0.03225 (  349)
  hydrogen bonds       : angle       5.40137 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9290 (mmm) cc_final: 0.8922 (mmm)
REVERT: A  203 MET cc_start: 0.9456 (mmm) cc_final: 0.8753 (mmm)
REVERT: A  346 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8140 (ptp)
REVERT: A  348 MET cc_start: 0.8519 (mpp) cc_final: 0.8277 (mpp)
REVERT: A  398 CYS cc_start: 0.8945 (m) cc_final: 0.8556 (t)
REVERT: B  115 MET cc_start: 0.7965 (ppp) cc_final: 0.7476 (ppp)
REVERT: B  212 MET cc_start: 0.9406 (tpp) cc_final: 0.9119 (tpp)
REVERT: B  357 MET cc_start: 0.8948 (mmm) cc_final: 0.8550 (tpp)
REVERT: B  479 THR cc_start: 0.9494 (OUTLIER) cc_final: 0.9290 (t)
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0642
  time to fit residues: 4.5444
Evaluate side-chains
  39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  346 MET
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  479 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 80 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   overall best weight:    2.5386

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.034523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.024901 restraints weight = 59227.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.025816 restraints weight = 30783.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.026442 restraints weight = 20602.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.026869 restraints weight = 15833.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.027169 restraints weight = 13327.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8239  Z= 0.134
  Angle     :  0.523   9.546  11149  Z= 0.262
  Chirality :  0.040   0.156   1267
  Planarity :  0.003   0.021   1424
  Dihedral  :  4.410  28.924   1143
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.23 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.27), residues: 1025
  helix:  2.05 (0.28), residues: 347
  sheet: -0.08 (0.41), residues: 164
  loop : -0.42 (0.29), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.010   0.001   TYR A  88 
 PHE   0.007   0.001   PHE A 211 
 TRP   0.011   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8239)
  covalent geometry    : angle       0.52299 (11149)
  hydrogen bonds       : bond        0.03021 (  349)
  hydrogen bonds       : angle       5.28272 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   48 MET cc_start: 0.9076 (mmm) cc_final: 0.8466 (mmt)
REVERT: A   62 MET cc_start: 0.9292 (mmm) cc_final: 0.8861 (mmm)
REVERT: A  203 MET cc_start: 0.9422 (mmm) cc_final: 0.8714 (mmm)
REVERT: A  348 MET cc_start: 0.8543 (mpp) cc_final: 0.8126 (mpp)
REVERT: A  514 MET cc_start: 0.9494 (ptp) cc_final: 0.9055 (ptp)
REVERT: B  115 MET cc_start: 0.8086 (ppp) cc_final: 0.7618 (ppp)
REVERT: B  212 MET cc_start: 0.9435 (tpp) cc_final: 0.9121 (tpp)
REVERT: B  357 MET cc_start: 0.8930 (mmm) cc_final: 0.8509 (tpp)
REVERT: B  479 THR cc_start: 0.9451 (OUTLIER) cc_final: 0.9240 (t)
  outliers start: 12
  outliers final: 7
  residues processed: 46
  average time/residue: 0.0605
  time to fit residues: 4.6716
Evaluate side-chains
  41 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  479 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 5 optimal weight:    0.0970
   chunk 39 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 46 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 69 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0060
   chunk 68 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    3.4200

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3015 r_free = 0.3015 target = 0.034331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.024782 restraints weight = 58811.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.025686 restraints weight = 30667.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.026307 restraints weight = 20556.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.026701 restraints weight = 15799.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.027011 restraints weight = 13419.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8239  Z= 0.169
  Angle     :  0.542   8.641  11149  Z= 0.269
  Chirality :  0.039   0.134   1267
  Planarity :  0.003   0.021   1424
  Dihedral  :  4.342  24.301   1143
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.05 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.71 (0.27), residues: 1025
  helix:  2.07 (0.28), residues: 347
  sheet: -0.17 (0.41), residues: 167
  loop : -0.39 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 232 
 TYR   0.009   0.001   TYR A 322 
 PHE   0.007   0.001   PHE B  59 
 TRP   0.012   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8239)
  covalent geometry    : angle       0.54236 (11149)
  hydrogen bonds       : bond        0.03048 (  349)
  hydrogen bonds       : angle       5.28716 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 32
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9312 (mmm) cc_final: 0.8848 (mmm)
REVERT: A  203 MET cc_start: 0.9422 (mmm) cc_final: 0.8745 (mmm)
REVERT: A  348 MET cc_start: 0.8452 (mpp) cc_final: 0.8171 (mpp)
REVERT: A  398 CYS cc_start: 0.8914 (m) cc_final: 0.8498 (t)
REVERT: B  115 MET cc_start: 0.8098 (ppp) cc_final: 0.7638 (ppp)
REVERT: B  212 MET cc_start: 0.9459 (tpp) cc_final: 0.9116 (tpp)
REVERT: B  357 MET cc_start: 0.8938 (mmm) cc_final: 0.8518 (tpp)
  outliers start: 11
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0623
  time to fit residues: 4.4282
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    0.0370
   chunk 76 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    1.2066

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3033 r_free = 0.3033 target = 0.034894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.025262 restraints weight = 59209.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.026194 restraints weight = 30498.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.026836 restraints weight = 20339.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.027275 restraints weight = 15627.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.027530 restraints weight = 13151.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8239  Z= 0.095
  Angle     :  0.527   8.928  11149  Z= 0.260
  Chirality :  0.040   0.137   1267
  Planarity :  0.003   0.023   1424
  Dihedral  :  4.160  20.308   1142
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 12.21 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 1025
  helix:  2.03 (0.28), residues: 349
  sheet:  0.07 (0.41), residues: 164
  loop : -0.37 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.013   0.001   TYR A  88 
 PHE   0.010   0.001   PHE B  59 
 TRP   0.016   0.001   TRP A 148 
 HIS   0.003   0.000   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 8239)
  covalent geometry    : angle       0.52724 (11149)
  hydrogen bonds       : bond        0.02823 (  349)
  hydrogen bonds       : angle       5.15094 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8955 (mmm) cc_final: 0.8347 (mmt)
REVERT: A   62 MET cc_start: 0.9318 (mmm) cc_final: 0.8813 (mmm)
REVERT: A  203 MET cc_start: 0.9381 (mmm) cc_final: 0.8679 (mmm)
REVERT: A  348 MET cc_start: 0.8410 (mpp) cc_final: 0.8132 (mpp)
REVERT: B  115 MET cc_start: 0.8261 (ppp) cc_final: 0.7838 (ppp)
REVERT: B  212 MET cc_start: 0.9461 (tpp) cc_final: 0.9111 (tpp)
  outliers start: 6
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0610
  time to fit residues: 4.2094
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    9.9990
   chunk 83 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   chunk 36 optimal weight:    0.9980
   overall best weight:    1.1962

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3027 r_free = 0.3027 target = 0.034890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.025298 restraints weight = 58025.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.026237 restraints weight = 30052.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.026879 restraints weight = 19993.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.027318 restraints weight = 15337.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.027570 restraints weight = 12878.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8863
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   8239  Z= 0.095
  Angle     :  0.531   9.808  11149  Z= 0.258
  Chirality :  0.039   0.137   1267
  Planarity :  0.003   0.023   1424
  Dihedral  :  4.052  19.825   1141
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 12.56 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.27), residues: 1025
  helix:  2.04 (0.28), residues: 349
  sheet:  0.09 (0.41), residues: 164
  loop : -0.34 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 497 
 TYR   0.008   0.001   TYR A  71 
 PHE   0.009   0.001   PHE B  59 
 TRP   0.020   0.002   TRP A 148 
 HIS   0.003   0.000   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 8239)
  covalent geometry    : angle       0.53095 (11149)
  hydrogen bonds       : bond        0.02787 (  349)
  hydrogen bonds       : angle       5.08696 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9308 (mmm) cc_final: 0.8798 (mmm)
REVERT: A  167 MET cc_start: 0.9334 (mtp) cc_final: 0.8642 (mpp)
REVERT: A  203 MET cc_start: 0.9329 (mmm) cc_final: 0.8661 (mmm)
REVERT: B  115 MET cc_start: 0.8366 (ppp) cc_final: 0.7963 (ppp)
REVERT: B  212 MET cc_start: 0.9464 (tpp) cc_final: 0.9110 (tpp)
  outliers start: 7
  outliers final: 6
  residues processed: 42
  average time/residue: 0.0611
  time to fit residues: 4.2993
Evaluate side-chains
  39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 VAL
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 94 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 54 optimal weight:    9.9990
   chunk 92 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.2965 r_free = 0.2965 target = 0.033876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.024043 restraints weight = 60225.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.024976 restraints weight = 32267.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.025617 restraints weight = 21923.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.026040 restraints weight = 17047.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026298 restraints weight = 14457.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8239  Z= 0.133
  Angle     :  0.578   9.938  11149  Z= 0.274
  Chirality :  0.039   0.135   1267
  Planarity :  0.003   0.021   1424
  Dihedral  :  4.061  19.813   1141
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 12.67 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.28), residues: 1025
  helix:  2.12 (0.28), residues: 349
  sheet:  0.16 (0.42), residues: 164
  loop : -0.28 (0.29), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 399 
 TYR   0.007   0.001   TYR A  71 
 PHE   0.010   0.001   PHE A 432 
 TRP   0.018   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8239)
  covalent geometry    : angle       0.57751 (11149)
  hydrogen bonds       : bond        0.02859 (  349)
  hydrogen bonds       : angle       5.07018 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8964 (mmm) cc_final: 0.8411 (mmm)
REVERT: A   62 MET cc_start: 0.9305 (mmm) cc_final: 0.8799 (mmm)
REVERT: A  167 MET cc_start: 0.9322 (mtp) cc_final: 0.8547 (mpp)
REVERT: A  203 MET cc_start: 0.9329 (mmm) cc_final: 0.8654 (mmm)
REVERT: A  514 MET cc_start: 0.9553 (ptp) cc_final: 0.9261 (ptp)
REVERT: B  115 MET cc_start: 0.8328 (ppp) cc_final: 0.7923 (ppp)
REVERT: B  212 MET cc_start: 0.9482 (tpp) cc_final: 0.9133 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 41
  average time/residue: 0.0654
  time to fit residues: 4.4243
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 101 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 17 optimal weight:    0.3980
   chunk 85 optimal weight:    1.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    4.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3215 r_free = 0.3215 target = 0.046801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.039305 restraints weight = 71601.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.040257 restraints weight = 31716.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.040918 restraints weight = 19083.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.041253 restraints weight = 13476.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.041491 restraints weight = 11059.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8239  Z= 0.203
  Angle     :  0.616  10.800  11149  Z= 0.297
  Chirality :  0.039   0.133   1267
  Planarity :  0.003   0.021   1424
  Dihedral  :  4.167  20.199   1141
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 13.14 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.28), residues: 1025
  helix:  2.16 (0.28), residues: 349
  sheet:  0.10 (0.42), residues: 171
  loop : -0.25 (0.30), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.012   0.001   TYR A 322 
 PHE   0.009   0.001   PHE A 432 
 TRP   0.017   0.002   TRP A 148 
 HIS   0.004   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 8239)
  covalent geometry    : angle       0.61597 (11149)
  hydrogen bonds       : bond        0.03001 (  349)
  hydrogen bonds       : angle       5.05665 (  984)

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

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

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2050 Ramachandran restraints generated.
    1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8846 (mmm) cc_final: 0.8599 (mmm)
REVERT: A   62 MET cc_start: 0.9241 (mmm) cc_final: 0.8734 (mmm)
REVERT: A  203 MET cc_start: 0.9270 (mmm) cc_final: 0.8619 (mmm)
REVERT: B  115 MET cc_start: 0.8150 (ppp) cc_final: 0.7711 (ppp)
REVERT: B  212 MET cc_start: 0.9316 (tpp) cc_final: 0.8996 (tpp)
REVERT: B  357 MET cc_start: 0.8895 (mmm) cc_final: 0.8542 (tpp)
  outliers start: 6
  outliers final: 4
  residues processed: 38
  average time/residue: 0.0646
  time to fit residues: 4.0533
Evaluate side-chains
  36 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  407 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 66 optimal weight:    7.9990
   chunk 58 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 16 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 101 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 416 GLN ** 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 = 0.3125 r_free = 0.3125 target = 0.036097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.026349 restraints weight = 58820.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.027284 restraints weight = 29610.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.027937 restraints weight = 19616.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.028365 restraints weight = 14970.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.028668 restraints weight = 12544.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8861
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8239  Z= 0.168
  Angle     :  0.609  10.802  11149  Z= 0.291
  Chirality :  0.040   0.134   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.172  20.436   1141
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 13.26 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.28), residues: 1025
  helix:  2.10 (0.28), residues: 349
  sheet:  0.16 (0.41), residues: 181
  loop : -0.27 (0.30), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.010   0.001   TYR A 322 
 PHE   0.007   0.001   PHE A 410 
 TRP   0.020   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8239)
  covalent geometry    : angle       0.60875 (11149)
  hydrogen bonds       : bond        0.02925 (  349)
  hydrogen bonds       : angle       5.04527 (  984)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1328.07 seconds
wall clock time: 23 minutes 41.41 seconds (1421.41 seconds total)