Starting phenix.real_space_refine
on Tue Feb 11 09:06:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pag_13269/02_2025/7pag_13269.cif"
  }
  resolution = 4.0
  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=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 971 atoms to isotropic.
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
     Ca      3      9.91       5
     S      28      5.16       5
     C    2504      2.51       5
     N     746      2.21       5
     O     759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4040
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 4023
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 23, 'TRANS': 485}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 17
          Unusual residues: {' CA': 3, 'NAG': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.26, per 1000 atoms: 0.81
  Number of scatterers: 4040
  At special positions: 0
  Unit cell: (91.12, 71.02, 171.52, 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)
     Ca      3     19.99
     S      28     16.00
     O     759      8.00
     N     746      7.00
     C    2504      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  75 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  30 " - pdb=" SG  CYS A  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 241 " - pdb=" SG  CYS A 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 256 " - pdb=" SG  CYS A 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 376 " - pdb=" SG  CYS A 392 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 380 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 396 " - pdb=" SG  CYS A 406 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 509 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 524 " - pdb=" SG  CYS A 533 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG A 604 " - " ASN A 204 "
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 455.6 milliseconds
  

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  956

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 6 sheets defined
      15.1% alpha, 54.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 43
    Processing helix  chain 'A' and resid 189 through 199
    Processing helix  chain 'A' and resid 204 through 219
      removed outlier: 4.372A  pdb=" N   HIS A 209 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ALA A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 217 " --> pdb=" O   ARG A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 312
    Processing helix  chain 'A' and resid 320 through 331
      removed outlier: 3.726A  pdb=" N   PHE A 324 " --> pdb=" O   THR A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 334
      No H-bonds generated for 'chain 'A' and resid 332 through 334'
    Processing helix  chain 'A' and resid 346 through 349
    Processing helix  chain 'A' and resid 353 through 355
      No H-bonds generated for 'chain 'A' and resid 353 through 355'
    Processing helix  chain 'A' and resid 356 through 373
      removed outlier: 3.773A  pdb=" N   GLN A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ALA A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   TRP A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47
      removed outlier: 3.564A  pdb=" N   HIS A 221 " --> pdb=" O   MET A  47 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA A 269 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 134
      removed outlier: 10.294A  pdb=" N   PHE A 180 " --> pdb=" O   PRO A  96 " (cutoff:3.500A)
      removed outlier: 9.087A  pdb=" N   SER A  98 " --> pdb=" O   TYR A 178 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   TYR A 178 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   HIS A 100 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   MET A 142 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   SER A 264 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   ALA A 144 " --> pdb=" O   GLN A 262 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   GLN A 262 " --> pdb=" O   ALA A 144 " (cutoff:3.500A)
      removed outlier: 4.696A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 260 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   GLU A 260 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   GLY A 148 " --> pdb=" O   ASN A 258 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   ASN A 258 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   HIS A 150 " --> pdb=" O   CYS A 256 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   CYS A 256 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LYS A 152 " --> pdb=" O   GLY A 254 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   GLY A 254 " --> pdb=" O   LYS A 152 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   ALA A 154 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   GLU A 252 " --> pdb=" O   ALA A 154 " (cutoff:3.500A)
      removed outlier: 5.375A  pdb=" N   PHE A 156 " --> pdb=" O   ALA A 250 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ALA A 250 " --> pdb=" O   PHE A 156 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ALA A 158 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   LEU A 248 " --> pdb=" O   ALA A 158 " (cutoff:3.500A)
      removed outlier: 5.280A  pdb=" N   LYS A 160 " --> pdb=" O   ASN A 246 " (cutoff:3.500A)
      removed outlier: 7.433A  pdb=" N   ASN A 246 " --> pdb=" O   LYS A 160 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   TYR A 162 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   THR A 244 " --> pdb=" O   TYR A 162 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   ASP A 164 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   GLN A 242 " --> pdb=" O   ASP A 164 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   TYR A 166 " --> pdb=" O   THR A 240 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   THR A 240 " --> pdb=" O   TYR A 166 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   PHE A 168 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   LEU A 238 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   SER A 170 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   THR A 236 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   THR A 172 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      removed outlier: 7.329A  pdb=" N   VAL A 234 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   GLU A 174 " --> pdb=" O   ILE A 232 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ILE A 232 " --> pdb=" O   GLU A 174 " (cutoff:3.500A)
      removed outlier: 5.182A  pdb=" N   ARG A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   GLY A 230 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   SER A 341 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 5.025A  pdb=" N   VAL A 226 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP A 339 " --> pdb=" O   VAL A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
      removed outlier: 4.348A  pdb=" N   THR A  73 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 459 through 460
      removed outlier: 4.182A  pdb=" N   PHE A 421 " --> pdb=" O   TRP A 460 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   VAL A 418 " --> pdb=" O   HIS A 521 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   HIS A 521 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   ASN A 420 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
      removed outlier: 4.296A  pdb=" N   SER A 519 " --> pdb=" O   ASN A 420 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 470
      removed outlier: 5.188A  pdb=" N   ASP A 465 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL A 418 " --> pdb=" O   ASP A 465 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLU A 467 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 416 " --> pdb=" O   GLU A 467 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LYS A 523 " --> pdb=" O   HIS A 415 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 448
      removed outlier: 6.633A  pdb=" N   LEU A 477 " --> pdb=" O   ASP A 497 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ASP A 497 " --> pdb=" O   LEU A 477 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   VAL A 479 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   SER A 495 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   VAL A 481 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP A 491 " --> pdb=" O   ASP A 483 " (cutoff:3.500A)

    143 hydrogen bonds defined for protein.
    405 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: 1.08

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 669
        1.32 -     1.45: 1180
        1.45 -     1.58: 2251
        1.58 -     1.71: 0
        1.71 -     1.84: 36
  Bond restraints: 4136
  Sorted by residual:
  bond pdb=" C7  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.346  1.463 -0.117 2.00e-02 2.50e+03 3.42e+01
  bond pdb=" C1  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.406  1.504 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" C5  NAG A 604 "
       pdb=" O5  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.413  1.474 -0.061 2.00e-02 2.50e+03 9.43e+00
  bond pdb=" C2  NAG A 604 "
       pdb=" N2  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.439  1.499 -0.060 2.00e-02 2.50e+03 9.08e+00
  bond pdb=" C3  NAG A 604 "
       pdb=" O3  NAG A 604 "
    ideal  model  delta    sigma   weight residual
    1.403  1.453 -0.050 2.00e-02 2.50e+03 6.19e+00
  ... (remaining 4131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 5355
        1.53 -     3.06: 197
        3.06 -     4.58: 39
        4.58 -     6.11: 19
        6.11 -     7.64: 1
  Bond angle restraints: 5611
  Sorted by residual:
  angle pdb=" N   ARG A 298 "
        pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     109.52  101.88    7.64 1.55e+00 4.16e-01 2.43e+01
  angle pdb=" CA  ARG A 298 "
        pdb=" C   ARG A 298 "
        pdb=" O   ARG A 298 "
      ideal   model   delta    sigma   weight residual
     121.44  116.82    4.62 1.17e+00 7.31e-01 1.56e+01
  angle pdb=" N   ASP A  82 "
        pdb=" CA  ASP A  82 "
        pdb=" C   ASP A  82 "
      ideal   model   delta    sigma   weight residual
     111.71  106.85    4.86 1.34e+00 5.57e-01 1.32e+01
  angle pdb=" N   VAL A 451 "
        pdb=" CA  VAL A 451 "
        pdb=" C   VAL A 451 "
      ideal   model   delta    sigma   weight residual
     107.37  111.93   -4.56 1.48e+00 4.57e-01 9.49e+00
  angle pdb=" C   CYS A 396 "
        pdb=" N   GLN A 397 "
        pdb=" CA  GLN A 397 "
      ideal   model   delta    sigma   weight residual
     121.54  126.90   -5.36 1.91e+00 2.74e-01 7.87e+00
  ... (remaining 5606 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 2246
       17.11 -    34.22: 203
       34.22 -    51.33: 45
       51.33 -    68.44: 7
       68.44 -    85.55: 7
  Dihedral angle restraints: 2508
    sinusoidal: 1030
      harmonic: 1478
  Sorted by residual:
  dihedral pdb=" CB  CYS A 376 "
           pdb=" SG  CYS A 376 "
           pdb=" SG  CYS A 392 "
           pdb=" CB  CYS A 392 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -4.35  -81.65     1      1.00e+01 1.00e-02 8.21e+01
  dihedral pdb=" CB  CYS A 396 "
           pdb=" SG  CYS A 396 "
           pdb=" SG  CYS A 406 "
           pdb=" CB  CYS A 406 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.15  -53.15     1      1.00e+01 1.00e-02 3.84e+01
  dihedral pdb=" CA  LEU A 359 "
           pdb=" C   LEU A 359 "
           pdb=" N   ARG A 360 "
           pdb=" CA  ARG A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 2505 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 370
       0.034 -    0.068: 156
       0.068 -    0.101: 48
       0.101 -    0.135: 26
       0.135 -    0.169: 4
  Chirality restraints: 604
  Sorted by residual:
  chirality pdb=" CA  ARG A 298 "
            pdb=" N   ARG A 298 "
            pdb=" C   ARG A 298 "
            pdb=" CB  ARG A 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  GLU A 446 "
            pdb=" N   GLU A 446 "
            pdb=" C   GLU A 446 "
            pdb=" CB  GLU A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.82e-01
  ... (remaining 601 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 499 "    0.050 5.00e-02 4.00e+02   7.67e-02 9.42e+00
        pdb=" N   PRO A 500 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 500 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 500 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  95 "   -0.050 5.00e-02 4.00e+02   7.63e-02 9.32e+00
        pdb=" N   PRO A  96 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A  96 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  96 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 407 "    0.041 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 408 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 408 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 408 "    0.034 5.00e-02 4.00e+02
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 184
        2.72 -     3.27: 3973
        3.27 -     3.81: 6105
        3.81 -     4.36: 6879
        4.36 -     4.90: 12259
  Nonbonded interactions: 29400
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 320 "
            pdb=" OE1 GLN A 323 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" O   TYR A 366 "
            pdb=" OG  SER A 369 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" OH  TYR A 366 "
            pdb=" NH1 ARG A 370 "
     model   vdw
     2.215 3.120
  nonbonded pdb=" OE2 GLU A 395 "
            pdb=" OG  SER A 399 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   GLN A 361 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.247 3.040
  ... (remaining 29395 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.270
  Find NCS groups from input model:        0.040
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5782
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.117   4136  Z= 0.316
  Angle     :  0.746   7.641   5611  Z= 0.411
  Chirality :  0.046   0.169    604
  Planarity :  0.006   0.077    738
  Dihedral  : 13.809  85.555   1525
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.35), residues: 505
  helix: -1.61 (0.67), residues: 55
  sheet:  0.15 (0.33), residues: 207
  loop : -2.22 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 327 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.016   0.002   PHE A 447 
 TYR   0.012   0.001   TYR A 437 
 ARG   0.006   0.001   ARG A 422 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 LEU cc_start: 0.8991 (tp) cc_final: 0.8630 (mp)
REVERT: A  231 ARG cc_start: 0.7457 (ttm170) cc_final: 0.7176 (ttt180)
REVERT: A  479 VAL cc_start: 0.9503 (t) cc_final: 0.9156 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.2226
  time to fit residues: 24.6936
Evaluate side-chains
  48 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 HIS
A 285 HIS
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 375 ASN
A 539 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5514 r_free = 0.5514 target = 0.363708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5406 r_free = 0.5406 target = 0.193460 restraints weight = 4420.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.5376 r_free = 0.5376 target = 0.180692 restraints weight = 7086.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 82)----------------|
| r_work = 0.5373 r_free = 0.5373 target = 0.169301 restraints weight = 4924.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.5057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069   4136  Z= 0.540
  Angle     :  0.986  10.958   5611  Z= 0.541
  Chirality :  0.054   0.218    604
  Planarity :  0.009   0.084    738
  Dihedral  :  7.136  28.165    579
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 23.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 10.73 %
    Favored  : 86.07 %
  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: -3.13 (0.35), residues: 505
  helix: -0.02 (0.72), residues: 51
  sheet: -2.30 (0.31), residues: 213
  loop : -2.22 (0.39), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 128 
 HIS   0.015   0.003   HIS A 292 
 PHE   0.032   0.003   PHE A 156 
 TYR   0.023   0.003   TYR A 275 
 ARG   0.010   0.001   ARG A 372 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 TYR cc_start: 0.7364 (p90) cc_final: 0.7022 (p90)
REVERT: A   81 ARG cc_start: 0.8194 (tpt90) cc_final: 0.7905 (tpt90)
REVERT: A  163 GLN cc_start: 0.8041 (pt0) cc_final: 0.7728 (tm-30)
REVERT: A  169 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8189 (p0)
REVERT: A  293 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.7015 (mp10)
REVERT: A  343 GLU cc_start: 0.8677 (tp30) cc_final: 0.8429 (tp30)
REVERT: A  366 TYR cc_start: 0.8366 (t80) cc_final: 0.8126 (t80)
REVERT: A  464 MET cc_start: 0.7410 (tpp) cc_final: 0.7152 (tpp)
  outliers start: 14
  outliers final: 8
  residues processed: 78
  average time/residue: 0.1680
  time to fit residues: 16.2668
Evaluate side-chains
  55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  293 GLN
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 7 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 17 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 49 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** 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 = 0.5498 r_free = 0.5498 target = 0.365746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5430 r_free = 0.5430 target = 0.228200 restraints weight = 4381.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5393 r_free = 0.5393 target = 0.186877 restraints weight = 5208.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 121)---------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.172479 restraints weight = 4362.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.5073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6682
moved from start:          0.5559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   4136  Z= 0.333
  Angle     :  0.852   9.211   5611  Z= 0.456
  Chirality :  0.051   0.181    604
  Planarity :  0.006   0.054    738
  Dihedral  :  6.348  24.202    579
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.67 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.18 (0.35), residues: 505
  helix: -0.72 (0.66), residues: 58
  sheet: -2.38 (0.33), residues: 213
  loop : -2.06 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 482 
 HIS   0.009   0.002   HIS A 285 
 PHE   0.025   0.002   PHE A 156 
 TYR   0.030   0.002   TYR A 166 
 ARG   0.004   0.001   ARG A 360 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
REVERT: A  163 GLN cc_start: 0.7944 (pt0) cc_final: 0.7375 (tm-30)
REVERT: A  240 THR cc_start: 0.8252 (p) cc_final: 0.7999 (m)
REVERT: A  257 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7372 (mp)
REVERT: A  372 ARG cc_start: 0.7363 (ppt170) cc_final: 0.6953 (ppt170)
REVERT: A  464 MET cc_start: 0.7399 (tpp) cc_final: 0.6904 (tpp)
  outliers start: 14
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2019
  time to fit residues: 15.7365
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** 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 = 0.5509 r_free = 0.5509 target = 0.375070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5471 r_free = 0.5471 target = 0.241918 restraints weight = 4391.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5498 r_free = 0.5498 target = 0.214208 restraints weight = 4911.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.5484 r_free = 0.5484 target = 0.199935 restraints weight = 4964.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.5144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6497
moved from start:          0.5903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4136  Z= 0.225
  Angle     :  0.747   8.990   5611  Z= 0.392
  Chirality :  0.049   0.301    604
  Planarity :  0.005   0.051    738
  Dihedral  :  5.261  19.510    579
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.72 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 15.98 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.35), residues: 505
  helix: -0.47 (0.68), residues: 58
  sheet: -2.08 (0.34), residues: 203
  loop : -1.92 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 482 
 HIS   0.004   0.001   HIS A 189 
 PHE   0.021   0.002   PHE A 518 
 TYR   0.015   0.002   TYR A 166 
 ARG   0.004   0.000   ARG A 478 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ARG cc_start: 0.8162 (tpt90) cc_final: 0.7931 (mmm160)
REVERT: A   98 SER cc_start: 0.6005 (p) cc_final: 0.5788 (m)
REVERT: A  231 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7587 (ttt-90)
REVERT: A  251 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.6583 (t70)
REVERT: A  372 ARG cc_start: 0.7671 (ppt170) cc_final: 0.7190 (ppt170)
REVERT: A  464 MET cc_start: 0.7284 (tpp) cc_final: 0.6525 (tpp)
REVERT: A  488 TRP cc_start: 0.4975 (p90) cc_final: 0.3696 (t60)
  outliers start: 9
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1869
  time to fit residues: 13.6404
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 4 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 7 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    3.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5461 r_free = 0.5461 target = 0.361290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.5372 r_free = 0.5372 target = 0.225452 restraints weight = 4522.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.5377 r_free = 0.5377 target = 0.192616 restraints weight = 5516.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.5367 r_free = 0.5367 target = 0.186128 restraints weight = 6325.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.5085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6636
moved from start:          0.6643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   4136  Z= 0.340
  Angle     :  0.879  15.539   5611  Z= 0.472
  Chirality :  0.050   0.193    604
  Planarity :  0.006   0.055    738
  Dihedral  :  6.284  24.518    579
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 18.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.41 %
    Favored  : 77.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.35), residues: 505
  helix: -0.94 (0.65), residues: 64
  sheet: -2.62 (0.33), residues: 199
  loop : -2.12 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 482 
 HIS   0.009   0.002   HIS A 285 
 PHE   0.020   0.002   PHE A 156 
 TYR   0.021   0.002   TYR A 162 
 ARG   0.004   0.000   ARG A  86 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8352 (tm-30) cc_final: 0.8130 (tm-30)
REVERT: A  169 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7885 (p0)
REVERT: A  251 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7195 (t70)
REVERT: A  464 MET cc_start: 0.7451 (tpp) cc_final: 0.6701 (tpp)
REVERT: A  477 LEU cc_start: 0.9110 (tt) cc_final: 0.8809 (mt)
REVERT: A  488 TRP cc_start: 0.5509 (p90) cc_final: 0.3449 (t60)
  outliers start: 13
  outliers final: 8
  residues processed: 55
  average time/residue: 0.2021
  time to fit residues: 14.0182
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 46 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5453 r_free = 0.5453 target = 0.360226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5362 r_free = 0.5362 target = 0.222323 restraints weight = 4394.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.181643 restraints weight = 5547.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.5314 r_free = 0.5314 target = 0.176468 restraints weight = 4615.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.5037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start:          0.6884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4136  Z= 0.316
  Angle     :  0.870  18.127   5611  Z= 0.467
  Chirality :  0.053   0.391    604
  Planarity :  0.005   0.055    738
  Dihedral  :  6.221  23.787    579
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 18.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.95 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.42 (0.35), residues: 505
  helix: -0.93 (0.64), residues: 64
  sheet: -2.73 (0.33), residues: 198
  loop : -2.10 (0.37), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 482 
 HIS   0.007   0.001   HIS A 285 
 PHE   0.022   0.002   PHE A 518 
 TYR   0.017   0.002   TYR A 275 
 ARG   0.009   0.001   ARG A 372 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.442 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8313 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: A  177 MET cc_start: 0.7603 (mmm) cc_final: 0.7264 (mmm)
REVERT: A  251 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7294 (t70)
REVERT: A  464 MET cc_start: 0.7455 (tpp) cc_final: 0.6695 (tpp)
REVERT: A  477 LEU cc_start: 0.9127 (tt) cc_final: 0.8844 (mt)
REVERT: A  488 TRP cc_start: 0.5796 (p90) cc_final: 0.3456 (t60)
REVERT: A  490 ASP cc_start: 0.2943 (OUTLIER) cc_final: 0.2423 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 58
  average time/residue: 0.2095
  time to fit residues: 15.0235
Evaluate side-chains
  47 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 35
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 20 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5460 r_free = 0.5460 target = 0.361403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5378 r_free = 0.5378 target = 0.224542 restraints weight = 4414.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5342 r_free = 0.5342 target = 0.183597 restraints weight = 5332.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5334 r_free = 0.5334 target = 0.177410 restraints weight = 4421.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.5052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.7076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   4136  Z= 0.264
  Angle     :  1.025  33.805   5611  Z= 0.518
  Chirality :  0.054   0.459    604
  Planarity :  0.005   0.054    738
  Dihedral  :  5.894  28.471    579
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 15.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 19.86 %
    Favored  : 76.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.35), residues: 505
  helix: -0.94 (0.64), residues: 64
  sheet: -2.47 (0.34), residues: 198
  loop : -2.03 (0.38), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 327 
 HIS   0.008   0.001   HIS A 189 
 PHE   0.020   0.002   PHE A 156 
 TYR   0.012   0.002   TYR A 166 
 ARG   0.005   0.000   ARG A  86 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 39
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7898 (tm-30)
REVERT: A  169 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.7941 (p0)
REVERT: A  177 MET cc_start: 0.7640 (mmm) cc_final: 0.7259 (mmm)
REVERT: A  251 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7355 (t70)
REVERT: A  477 LEU cc_start: 0.9191 (tt) cc_final: 0.8916 (mt)
REVERT: A  488 TRP cc_start: 0.5924 (p90) cc_final: 0.3458 (t60)
REVERT: A  490 ASP cc_start: 0.2999 (OUTLIER) cc_final: 0.2724 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1836
  time to fit residues: 11.8245
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 40 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 7 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5406 r_free = 0.5406 target = 0.349090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.5270 r_free = 0.5270 target = 0.204269 restraints weight = 4435.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.5241 r_free = 0.5241 target = 0.174240 restraints weight = 5718.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.5231 r_free = 0.5231 target = 0.168683 restraints weight = 6759.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.5007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
moved from start:          0.7700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   4136  Z= 0.452
  Angle     :  1.141  31.473   5611  Z= 0.599
  Chirality :  0.058   0.488    604
  Planarity :  0.007   0.046    738
  Dihedral  :  7.028  29.398    579
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 22.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.47 %
    Favored  : 86.53 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 19.18 %
    Favored  : 76.26 %
  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: -3.83 (0.34), residues: 505
  helix: -1.18 (0.61), residues: 64
  sheet: -3.09 (0.33), residues: 193
  loop : -2.33 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP A 482 
 HIS   0.011   0.002   HIS A 150 
 PHE   0.025   0.003   PHE A 518 
 TYR   0.026   0.003   TYR A 166 
 ARG   0.005   0.001   ARG A  86 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 42
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 TYR cc_start: 0.7520 (p90) cc_final: 0.7250 (p90)
REVERT: A  169 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8077 (p0)
REVERT: A  257 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7363 (mp)
REVERT: A  262 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.6538 (tm-30)
REVERT: A  477 LEU cc_start: 0.9202 (tt) cc_final: 0.8977 (mt)
REVERT: A  488 TRP cc_start: 0.6116 (p90) cc_final: 0.3972 (t60)
REVERT: A  490 ASP cc_start: 0.3390 (OUTLIER) cc_final: 0.2655 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 56
  average time/residue: 0.1630
  time to fit residues: 11.7327
Evaluate side-chains
  54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  191 ASP
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  262 GLN
Chi-restraints excluded: chain A residue  285 HIS
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  490 ASP
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0050
   chunk 5 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 19 optimal weight:    7.9990
   chunk 6 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 2 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   overall best weight:    1.9800

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** 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 = 0.5453 r_free = 0.5453 target = 0.359356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5365 r_free = 0.5365 target = 0.220516 restraints weight = 4391.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.5325 r_free = 0.5325 target = 0.180060 restraints weight = 5438.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.5315 r_free = 0.5315 target = 0.172180 restraints weight = 4566.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.5042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.7670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4136  Z= 0.258
  Angle     :  1.008  29.643   5611  Z= 0.513
  Chirality :  0.055   0.463    604
  Planarity :  0.005   0.045    738
  Dihedral  :  6.148  28.882    579
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 21.23 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.35), residues: 505
  helix: -0.86 (0.65), residues: 58
  sheet: -2.61 (0.33), residues: 209
  loop : -2.15 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 482 
 HIS   0.006   0.001   HIS A 189 
 PHE   0.023   0.002   PHE A 156 
 TYR   0.012   0.002   TYR A 162 
 ARG   0.004   0.000   ARG A  86 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ASN cc_start: 0.8367 (OUTLIER) cc_final: 0.7999 (p0)
REVERT: A  251 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7371 (t70)
REVERT: A  311 HIS cc_start: 0.7972 (m170) cc_final: 0.7483 (m-70)
REVERT: A  368 MET cc_start: 0.8699 (mpp) cc_final: 0.8393 (pmm)
REVERT: A  477 LEU cc_start: 0.9215 (tt) cc_final: 0.8971 (mt)
REVERT: A  488 TRP cc_start: 0.6041 (p90) cc_final: 0.3905 (t60)
REVERT: A  490 ASP cc_start: 0.3513 (OUTLIER) cc_final: 0.2761 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 52
  average time/residue: 0.2244
  time to fit residues: 14.7912
Evaluate side-chains
  50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 37
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  180 PHE
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** 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 = 0.5452 r_free = 0.5452 target = 0.361259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5372 r_free = 0.5372 target = 0.226088 restraints weight = 4376.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.5388 r_free = 0.5388 target = 0.194154 restraints weight = 5191.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.5386 r_free = 0.5386 target = 0.193413 restraints weight = 6037.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.5115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.7716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4136  Z= 0.245
  Angle     :  0.962  27.751   5611  Z= 0.490
  Chirality :  0.054   0.449    604
  Planarity :  0.005   0.047    738
  Dihedral  :  5.854  25.554    579
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.32 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.22 (0.36), residues: 505
  helix: -0.80 (0.66), residues: 58
  sheet: -2.40 (0.33), residues: 209
  loop : -2.09 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 482 
 HIS   0.006   0.001   HIS A 189 
 PHE   0.026   0.002   PHE A 518 
 TYR   0.015   0.002   TYR A 536 
 ARG   0.005   0.000   ARG A  70 

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

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

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1010 Ramachandran restraints generated.
    505 Oldfield, 0 Emsley, 505 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7542 (p0)
REVERT: A  251 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7378 (t70)
REVERT: A  276 LYS cc_start: 0.8616 (mttt) cc_final: 0.7775 (tmtt)
REVERT: A  311 HIS cc_start: 0.7605 (m170) cc_final: 0.7355 (m-70)
REVERT: A  477 LEU cc_start: 0.9216 (tt) cc_final: 0.8981 (mt)
REVERT: A  488 TRP cc_start: 0.6117 (p90) cc_final: 0.3818 (t60)
REVERT: A  490 ASP cc_start: 0.3388 (OUTLIER) cc_final: 0.2673 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 55
  average time/residue: 0.1979
  time to fit residues: 13.5203
Evaluate side-chains
  55 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLU
Chi-restraints excluded: chain A residue  162 TYR
Chi-restraints excluded: chain A residue  169 ASN
Chi-restraints excluded: chain A residue  171 ASP
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  251 ASP
Chi-restraints excluded: chain A residue  255 ASP
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  313 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  359 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  490 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0040
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    2.1998

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

Flipped N/Q/H residues before XYZ refinement:
** A 299 HIS ** 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 = 0.5449 r_free = 0.5449 target = 0.361068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.5367 r_free = 0.5367 target = 0.225330 restraints weight = 4393.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.193653 restraints weight = 5253.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.5363 r_free = 0.5363 target = 0.188712 restraints weight = 5996.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.5090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6600
moved from start:          0.7906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4136  Z= 0.255
  Angle     :  0.978  27.767   5611  Z= 0.494
  Chirality :  0.054   0.430    604
  Planarity :  0.005   0.047    738
  Dihedral  :  5.954  22.866    579
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 20.09 %
    Favored  : 76.26 %
  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: -3.16 (0.36), residues: 505
  helix: -0.80 (0.65), residues: 58
  sheet: -2.36 (0.34), residues: 214
  loop : -2.02 (0.39), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 482 
 HIS   0.007   0.001   HIS A 189 
 PHE   0.019   0.002   PHE A 156 
 TYR   0.012   0.002   TYR A 275 
 ARG   0.006   0.000   ARG A  70 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1645.03 seconds
wall clock time: 30 minutes 32.87 seconds (1832.87 seconds total)