Starting phenix.real_space_refine
on Wed Feb 12 16:20:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zt6_14955/02_2025/7zt6_14955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zt6_14955/02_2025/7zt6_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_14955/02_2025/7zt6_14955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zt6_14955/02_2025/7zt6_14955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zt6_14955/02_2025/7zt6_14955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zt6_14955/02_2025/7zt6_14955.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.008
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10}
          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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4}
          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: 5.38, per 1000 atoms: 0.67
  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: 2.35
  Conformation dependent library (CDL) restraints added in 990.8 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: 0.99
  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: 2.58

  Time building geometry restraints manager: 2.67 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:             2.210
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.640
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.690
-------------------------------------------------------------------------------
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= 0.398
  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 (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 (0.27), 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
 TRP   0.011   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B 131 
 PHE   0.015   0.001   PHE B 135 
 TYR   0.028   0.002   TYR A  71 
 ARG   0.003   0.000   ARG B  81 

*********************** 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  : 1.001 
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: 0.8205 (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: 0.8794 (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: 0.1952
  time to fit residues: 13.3742
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  : 0.922 
-------------------------------------------------------------------------------
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 86 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    9.9990
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 41 optimal weight:   20.0000
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 60 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   overall best weight:    3.7588

-------------------------------------------------------------------------------
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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.033714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.024038 restraints weight = 59098.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.024947 restraints weight = 31431.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.025562 restraints weight = 21277.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8879
moved from start:          0.0950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8239  Z= 0.266
  Angle     :  0.584   7.873  11149  Z= 0.296
  Chirality :  0.041   0.138   1267
  Planarity :  0.003   0.036   1424
  Dihedral  :  5.101  51.870   1143
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  5.93 %
    Favored  : 93.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.27), residues: 1025
  helix:  1.91 (0.28), residues: 339
  sheet: -0.38 (0.39), residues: 181
  loop : -0.52 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B  80 
 PHE   0.012   0.001   PHE B 135 
 TYR   0.017   0.001   TYR A  71 
 ARG   0.003   0.000   ARG B  81 

*********************** 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
  44 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 37
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A   48 MET cc_start: 0.9165 (mmt) cc_final: 0.8954 (mmm)
REVERT: A   62 MET cc_start: 0.9350 (mmp) cc_final: 0.9147 (mmm)
REVERT: A  346 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8404 (ptp)
REVERT: A  348 MET cc_start: 0.8710 (mpp) cc_final: 0.8366 (mpp)
REVERT: A  398 CYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8627 (t)
REVERT: B   13 CYS cc_start: 0.9319 (t) cc_final: 0.9100 (t)
REVERT: B  115 MET cc_start: 0.7804 (ppp) cc_final: 0.7392 (ppp)
REVERT: B  479 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9199 (t)
  outliers start: 7
  outliers final: 1
  residues processed: 39
  average time/residue: 0.1534
  time to fit residues: 9.9718
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  : 0.946 
-------------------------------------------------------------------------------
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  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 60 optimal weight:   10.0000
   chunk 12 optimal weight:   20.0000
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:    7.9990
   chunk 78 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0970
   chunk 90 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 46 optimal weight:    0.0060
   overall best weight:    3.0198

-------------------------------------------------------------------------------
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**
B 527 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.034077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.024383 restraints weight = 59779.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.025304 restraints weight = 31093.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.025930 restraints weight = 20765.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8902
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8239  Z= 0.219
  Angle     :  0.539   8.113  11149  Z= 0.273
  Chirality :  0.040   0.136   1267
  Planarity :  0.003   0.024   1424
  Dihedral  :  4.777  43.941   1143
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.60 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.28), residues: 1025
  helix:  2.12 (0.28), residues: 339
  sheet: -0.20 (0.40), residues: 177
  loop : -0.51 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.008   0.001   PHE A  49 
 TYR   0.013   0.001   TYR A  71 
 ARG   0.002   0.000   ARG B 497 

*********************** 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: 6
    poor density    : 36
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9343 (mmp) cc_final: 0.9108 (mmm)
REVERT: A  203 MET cc_start: 0.9614 (mmt) cc_final: 0.8874 (mmm)
REVERT: A  346 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8251 (ptp)
REVERT: A  348 MET cc_start: 0.8675 (mpp) cc_final: 0.8189 (mpp)
REVERT: A  398 CYS cc_start: 0.8972 (m) cc_final: 0.8588 (t)
REVERT: B  115 MET cc_start: 0.7903 (ppp) cc_final: 0.7403 (ppp)
REVERT: B  212 MET cc_start: 0.9359 (tpp) cc_final: 0.9139 (tpp)
REVERT: B  357 MET cc_start: 0.8868 (mmm) cc_final: 0.8445 (tpp)
REVERT: B  479 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9241 (t)
  outliers start: 6
  outliers final: 3
  residues processed: 41
  average time/residue: 0.1545
  time to fit residues: 10.5674
Evaluate side-chains
  36 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
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  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 78 optimal weight:    9.9990
   chunk 34 optimal weight:   10.0000
   chunk 16 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 91 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 85 optimal weight:    0.0470
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    3.4084

-------------------------------------------------------------------------------
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 509 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 = 0.3030 r_free = 0.3030 target = 0.034546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.024999 restraints weight = 59157.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2676 r_free = 0.2676 target = 0.025888 restraints weight = 30346.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.026449 restraints weight = 20357.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.2606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8914
moved from start:          0.1395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8239  Z= 0.235
  Angle     :  0.525   6.937  11149  Z= 0.265
  Chirality :  0.039   0.134   1267
  Planarity :  0.003   0.023   1424
  Dihedral  :  4.565  35.780   1143
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.00 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1025
  helix:  2.07 (0.28), residues: 347
  sheet: -0.15 (0.41), residues: 164
  loop : -0.46 (0.29), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.010   0.001   PHE B  59 
 TYR   0.010   0.001   TYR A  71 
 ARG   0.002   0.000   ARG B 497 

*********************** 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
  44 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9358 (mmp) cc_final: 0.9106 (mmm)
REVERT: A  167 MET cc_start: 0.9419 (mtp) cc_final: 0.9075 (mtt)
REVERT: A  203 MET cc_start: 0.9584 (mmt) cc_final: 0.8808 (mmm)
REVERT: A  346 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8156 (ptp)
REVERT: A  348 MET cc_start: 0.8569 (mpp) cc_final: 0.8292 (mpp)
REVERT: A  398 CYS cc_start: 0.8958 (m) cc_final: 0.8585 (t)
REVERT: B  115 MET cc_start: 0.7914 (ppp) cc_final: 0.7431 (ppp)
REVERT: B  212 MET cc_start: 0.9412 (tpp) cc_final: 0.9127 (tpp)
REVERT: B  357 MET cc_start: 0.8873 (mmm) cc_final: 0.8557 (tpp)
REVERT: B  479 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9293 (t)
  outliers start: 8
  outliers final: 5
  residues processed: 43
  average time/residue: 0.1648
  time to fit residues: 11.5069
Evaluate side-chains
  40 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
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 A residue  522 VAL
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 32 optimal weight:    7.9990
   chunk 13 optimal weight:    9.9990
   chunk 57 optimal weight:    7.9990
   chunk 88 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 66 optimal weight:    0.2980
   chunk 100 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 73 optimal weight:    9.9990
   chunk 44 optimal weight:    9.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
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 509 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 = 0.3003 r_free = 0.3003 target = 0.034312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.024720 restraints weight = 58387.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.025644 restraints weight = 30424.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.026249 restraints weight = 20320.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8239  Z= 0.159
  Angle     :  0.520   8.587  11149  Z= 0.258
  Chirality :  0.040   0.137   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.417  29.477   1143
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.40 %
    Favored  : 87.33 %
  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:  0.74 (0.27), residues: 1025
  helix:  2.10 (0.28), residues: 347
  sheet: -0.05 (0.41), residues: 164
  loop : -0.42 (0.29), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.006   0.001   PHE A 211 
 TYR   0.011   0.001   TYR A  88 
 ARG   0.004   0.000   ARG B 232 

*********************** 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: 11
    poor density    : 36
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9360 (mmp) cc_final: 0.9101 (mmm)
REVERT: A  167 MET cc_start: 0.9429 (mtp) cc_final: 0.9120 (mtt)
REVERT: A  203 MET cc_start: 0.9541 (mmt) cc_final: 0.8807 (mmm)
REVERT: A  348 MET cc_start: 0.8576 (mpp) cc_final: 0.8140 (mpp)
REVERT: B  115 MET cc_start: 0.8104 (ppp) cc_final: 0.7652 (ppp)
REVERT: B  212 MET cc_start: 0.9457 (tpp) cc_final: 0.9141 (tpp)
REVERT: B  357 MET cc_start: 0.8850 (mmm) cc_final: 0.8612 (ttm)
REVERT: B  479 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9229 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 45
  average time/residue: 0.1612
  time to fit residues: 11.7987
Evaluate side-chains
  40 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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 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 54 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 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 = 0.3212 r_free = 0.3212 target = 0.046786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.039265 restraints weight = 71601.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.040229 restraints weight = 31599.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.040857 restraints weight = 18777.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8885
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8239  Z= 0.286
  Angle     :  0.564   8.319  11149  Z= 0.279
  Chirality :  0.039   0.133   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.420  24.805   1143
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.74 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.28), residues: 1025
  helix:  2.16 (0.28), residues: 347
  sheet: -0.16 (0.41), residues: 171
  loop : -0.39 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 148 
 HIS   0.004   0.001   HIS B 414 
 PHE   0.008   0.001   PHE B 426 
 TYR   0.011   0.001   TYR A 322 
 ARG   0.007   0.000   ARG B 232 

*********************** 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  : 0.956 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9291 (mmp) cc_final: 0.9073 (mmm)
REVERT: A  203 MET cc_start: 0.9454 (mmt) cc_final: 0.8717 (mmm)
REVERT: A  348 MET cc_start: 0.8410 (mpp) cc_final: 0.8152 (mpp)
REVERT: A  398 CYS cc_start: 0.8887 (m) cc_final: 0.8482 (t)
REVERT: B  115 MET cc_start: 0.7941 (ppp) cc_final: 0.7464 (ppp)
REVERT: B  212 MET cc_start: 0.9298 (tpp) cc_final: 0.8978 (tpp)
  outliers start: 11
  outliers final: 5
  residues processed: 43
  average time/residue: 0.1502
  time to fit residues: 10.6369
Evaluate side-chains
  37 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 VAL
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 4 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0870
   chunk 65 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 50 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    3.8166

-------------------------------------------------------------------------------
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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 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 = 0.2975 r_free = 0.2975 target = 0.033795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.024108 restraints weight = 59693.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.025019 restraints weight = 31286.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.025623 restraints weight = 21080.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8921
moved from start:          0.1738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8239  Z= 0.258
  Angle     :  0.575   9.587  11149  Z= 0.281
  Chirality :  0.040   0.134   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.375  21.634   1142
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.67 %
    Favored  : 86.28 %
  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:  0.77 (0.27), residues: 1025
  helix:  2.14 (0.28), residues: 347
  sheet: -0.13 (0.41), residues: 171
  loop : -0.39 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.008   0.001   PHE A 410 
 TYR   0.010   0.001   TYR A  88 
 ARG   0.002   0.000   ARG B  81 

*********************** 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
  43 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A   48 MET cc_start: 0.9065 (mmm) cc_final: 0.8476 (mmm)
REVERT: A   62 MET cc_start: 0.9383 (mmp) cc_final: 0.9121 (mmm)
REVERT: A  203 MET cc_start: 0.9551 (mmt) cc_final: 0.8815 (mmm)
REVERT: A  348 MET cc_start: 0.8452 (mpp) cc_final: 0.8156 (mpp)
REVERT: A  398 CYS cc_start: 0.8944 (m) cc_final: 0.8521 (t)
REVERT: B  115 MET cc_start: 0.8006 (ppp) cc_final: 0.7562 (ppp)
REVERT: B  212 MET cc_start: 0.9500 (tpp) cc_final: 0.9145 (tpp)
  outliers start: 9
  outliers final: 7
  residues processed: 42
  average time/residue: 0.1524
  time to fit residues: 10.6546
Evaluate side-chains
  39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 70 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 84 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 80 optimal weight:   20.0000
   chunk 23 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    3.8988

-------------------------------------------------------------------------------
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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 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 = 0.3046 r_free = 0.3046 target = 0.034804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.025195 restraints weight = 59775.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.026115 restraints weight = 30579.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.026742 restraints weight = 20364.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8917
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8239  Z= 0.264
  Angle     :  0.582   9.575  11149  Z= 0.286
  Chirality :  0.040   0.134   1267
  Planarity :  0.003   0.023   1424
  Dihedral  :  4.358  21.658   1142
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.14 %
    Favored  : 86.05 %
  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:  0.79 (0.27), residues: 1025
  helix:  2.17 (0.28), residues: 347
  sheet: -0.13 (0.41), residues: 171
  loop : -0.37 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.009   0.001   PHE A 410 
 TYR   0.010   0.001   TYR A 322 
 ARG   0.002   0.000   ARG B  81 

*********************** 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
  39 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A   62 MET cc_start: 0.9391 (mmp) cc_final: 0.9120 (mmm)
REVERT: A  167 MET cc_start: 0.9462 (mtp) cc_final: 0.9130 (mtt)
REVERT: A  203 MET cc_start: 0.9545 (mmt) cc_final: 0.8841 (mmm)
REVERT: A  348 MET cc_start: 0.8449 (mpp) cc_final: 0.8165 (mpp)
REVERT: A  398 CYS cc_start: 0.8957 (m) cc_final: 0.8525 (t)
REVERT: B  115 MET cc_start: 0.8025 (ppp) cc_final: 0.7593 (ppp)
REVERT: B  212 MET cc_start: 0.9502 (tpp) cc_final: 0.9146 (tpp)
  outliers start: 7
  outliers final: 6
  residues processed: 39
  average time/residue: 0.1702
  time to fit residues: 10.8821
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  : 0.946 
-------------------------------------------------------------------------------
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 64 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 18 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 99 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 52 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    3.3588

-------------------------------------------------------------------------------
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  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 509 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 = 0.3116 r_free = 0.3116 target = 0.035905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.026194 restraints weight = 60035.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.027142 restraints weight = 29821.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.027778 restraints weight = 19575.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8882
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8239  Z= 0.236
  Angle     :  0.588   9.775  11149  Z= 0.286
  Chirality :  0.040   0.134   1267
  Planarity :  0.003   0.022   1424
  Dihedral  :  4.365  21.835   1141
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  : 13.60 %
    Favored  : 85.58 %
  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:  0.80 (0.27), residues: 1025
  helix:  2.17 (0.28), residues: 347
  sheet: -0.16 (0.40), residues: 171
  loop : -0.35 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.009   0.001   PHE B 426 
 TYR   0.010   0.001   TYR A 322 
 ARG   0.002   0.000   ARG B  81 

*********************** 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: 7
    poor density    : 34
  time to evaluate  : 1.047 
Fit side-chains
REVERT: A   48 MET cc_start: 0.9043 (mmm) cc_final: 0.8416 (mmm)
REVERT: A   62 MET cc_start: 0.9401 (mmp) cc_final: 0.9124 (mmm)
REVERT: A  167 MET cc_start: 0.9549 (mtp) cc_final: 0.8691 (mpp)
REVERT: A  203 MET cc_start: 0.9555 (mmt) cc_final: 0.8873 (mmm)
REVERT: A  348 MET cc_start: 0.8446 (mpp) cc_final: 0.8176 (mpp)
REVERT: A  398 CYS cc_start: 0.9039 (m) cc_final: 0.8521 (t)
REVERT: A  514 MET cc_start: 0.9653 (ptp) cc_final: 0.9321 (ptp)
REVERT: B  115 MET cc_start: 0.8015 (ppp) cc_final: 0.7605 (ppp)
REVERT: B  212 MET cc_start: 0.9529 (tpp) cc_final: 0.9167 (tpp)
  outliers start: 7
  outliers final: 6
  residues processed: 40
  average time/residue: 0.1632
  time to fit residues: 10.7452
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  : 1.017 
-------------------------------------------------------------------------------
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   14 MET
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  321 VAL
Chi-restraints excluded: chain B residue  351 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 90 optimal weight:    7.9990
   chunk 19 optimal weight:    0.0270
   chunk 53 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   overall best weight:    3.2046

-------------------------------------------------------------------------------
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 = 0.3223 r_free = 0.3223 target = 0.047284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.039663 restraints weight = 71168.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.040642 restraints weight = 31270.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.041279 restraints weight = 18501.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8239  Z= 0.231
  Angle     :  0.608  11.935  11149  Z= 0.292
  Chirality :  0.040   0.135   1267
  Planarity :  0.003   0.023   1424
  Dihedral  :  4.302  21.135   1141
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.37 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.81 (0.28), residues: 1025
  helix:  2.12 (0.28), residues: 349
  sheet: -0.11 (0.41), residues: 171
  loop : -0.32 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.007   0.001   PHE B 356 
 TYR   0.009   0.001   TYR A 322 
 ARG   0.002   0.000   ARG B  81 

********************** 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
  41 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 1.244 
Fit side-chains
REVERT: A   48 MET cc_start: 0.8814 (mmm) cc_final: 0.8410 (mmm)
REVERT: A   62 MET cc_start: 0.9286 (mmp) cc_final: 0.9061 (mmm)
REVERT: A  167 MET cc_start: 0.9387 (mtp) cc_final: 0.8636 (mpp)
REVERT: A  203 MET cc_start: 0.9408 (mmt) cc_final: 0.8739 (mmm)
REVERT: A  348 MET cc_start: 0.8366 (mpp) cc_final: 0.8133 (mpp)
REVERT: A  398 CYS cc_start: 0.8893 (m) cc_final: 0.8478 (t)
REVERT: B  115 MET cc_start: 0.8043 (ppp) cc_final: 0.7595 (ppp)
REVERT: B  212 MET cc_start: 0.9307 (tpp) cc_final: 0.8983 (tpp)
  outliers start: 8
  outliers final: 7
  residues processed: 40
  average time/residue: 0.1734
  time to fit residues: 11.6853
Evaluate side-chains
  38 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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   14 MET
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 3 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 18 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    3.5990

-------------------------------------------------------------------------------
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  75 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 = 0.3219 r_free = 0.3219 target = 0.047111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.039481 restraints weight = 71196.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.040449 restraints weight = 31430.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.041121 restraints weight = 18640.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8239  Z= 0.256
  Angle     :  0.625  15.426  11149  Z= 0.298
  Chirality :  0.040   0.134   1267
  Planarity :  0.003   0.026   1424
  Dihedral  :  4.342  21.126   1141
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.49 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.28), residues: 1025
  helix:  2.10 (0.28), residues: 349
  sheet: -0.04 (0.41), residues: 171
  loop : -0.33 (0.29), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP A 148 
 HIS   0.003   0.001   HIS B 131 
 PHE   0.008   0.001   PHE B 356 
 TYR   0.010   0.001   TYR A 322 
 ARG   0.002   0.000   ARG B  81 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2228.49 seconds
wall clock time: 40 minutes 56.50 seconds (2456.50 seconds total)