Starting phenix.real_space_refine
on Thu Jul 24 09:44:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hiy_34829/07_2025/8hiy_34829.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3850      2.51       5
     N     952      2.21       5
     O    1058      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5890
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2945
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 12, 'TRANS': 371}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 94
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 81
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 61
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.93, per 1000 atoms: 0.84
  Number of scatterers: 5890
  At special positions: 0
  Unit cell: (83.3525, 83.3525, 108.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1058      8.00
     N     952      7.00
     C    3850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.43
  Conformation dependent library (CDL) restraints added in 687.3 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      82.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 84
    Processing helix  chain 'A' and resid 86 through 106
    Processing helix  chain 'A' and resid 111 through 128
    Processing helix  chain 'A' and resid 132 through 160
    Processing helix  chain 'A' and resid 168 through 188
      removed outlier: 4.270A  pdb=" N   SER A 175 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 176 " --> pdb=" O   CYS A 172 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A 188 " --> pdb=" O   THR A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 216
      removed outlier: 3.538A  pdb=" N   PHE A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 244
      removed outlier: 3.926A  pdb=" N   ILE A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   SER A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A 229 " --> pdb=" O   SER A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 276
      removed outlier: 3.652A  pdb=" N   VAL A 258 " --> pdb=" O   HIS A 254 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS A 259 " --> pdb=" O   ASN A 255 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   MET A 262 " --> pdb=" O   VAL A 258 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER A 267 " --> pdb=" O   ASN A 263 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 276 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
      removed outlier: 3.901A  pdb=" N   TYR A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 320
      removed outlier: 4.494A  pdb=" N   GLU A 313 " --> pdb=" O   THR A 309 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   SER A 314 " --> pdb=" O   SER A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 359
      removed outlier: 3.550A  pdb=" N   SER A 342 " --> pdb=" O   TYR A 338 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   THR A 351 " --> pdb=" O   HIS A 347 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL A 352 " --> pdb=" O   CYS A 348 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 371
      removed outlier: 3.569A  pdb=" N   GLN A 371 " --> pdb=" O   GLU A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 398
      removed outlier: 3.740A  pdb=" N   ARG A 379 " --> pdb=" O   GLN A 375 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   VAL A 380 " --> pdb=" O   GLU A 376 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 425
      removed outlier: 3.694A  pdb=" N   HIS A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP A 422 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LYS A 423 " --> pdb=" O   HIS A 419 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS A 424 " --> pdb=" O   LYS A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 428
      No H-bonds generated for 'chain 'A' and resid 426 through 428'
    Processing helix  chain 'A' and resid 531 through 536
    Processing helix  chain 'A' and resid 537 through 564
      removed outlier: 3.821A  pdb=" N   LEU A 543 " --> pdb=" O   THR A 539 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN A 552 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ASN A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 84
    Processing helix  chain 'B' and resid 86 through 106
    Processing helix  chain 'B' and resid 111 through 128
    Processing helix  chain 'B' and resid 132 through 160
    Processing helix  chain 'B' and resid 168 through 188
      removed outlier: 4.270A  pdb=" N   SER B 175 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE B 176 " --> pdb=" O   CYS B 172 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 177 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU B 188 " --> pdb=" O   THR B 184 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 216
      removed outlier: 3.537A  pdb=" N   PHE B 199 " --> pdb=" O   TYR B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 244
      removed outlier: 3.926A  pdb=" N   ILE B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
      removed outlier: 4.699A  pdb=" N   SER B 225 " --> pdb=" O   GLU B 221 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B 229 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 276
      removed outlier: 3.652A  pdb=" N   VAL B 258 " --> pdb=" O   HIS B 254 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LYS B 259 " --> pdb=" O   ASN B 255 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   MET B 262 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER B 267 " --> pdb=" O   ASN B 263 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   LEU B 276 " --> pdb=" O   VAL B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 308
      removed outlier: 3.901A  pdb=" N   TYR B 302 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 320
      removed outlier: 4.494A  pdb=" N   GLU B 313 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   SER B 314 " --> pdb=" O   SER B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 359
      removed outlier: 3.551A  pdb=" N   SER B 342 " --> pdb=" O   TYR B 338 " (cutoff:3.500A)
      removed outlier: 4.704A  pdb=" N   THR B 351 " --> pdb=" O   HIS B 347 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   VAL B 352 " --> pdb=" O   CYS B 348 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ILE B 359 " --> pdb=" O   LEU B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 371
      removed outlier: 3.569A  pdb=" N   GLN B 371 " --> pdb=" O   GLU B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 373 through 398
      removed outlier: 3.741A  pdb=" N   ARG B 379 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL B 380 " --> pdb=" O   GLU B 376 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LYS B 396 " --> pdb=" O   GLY B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 425
      removed outlier: 3.694A  pdb=" N   HIS B 411 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ASP B 422 " --> pdb=" O   GLN B 418 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   LYS B 423 " --> pdb=" O   HIS B 419 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS B 424 " --> pdb=" O   LYS B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 426 through 428
      No H-bonds generated for 'chain 'B' and resid 426 through 428'
    Processing helix  chain 'B' and resid 531 through 536
    Processing helix  chain 'B' and resid 537 through 564
      removed outlier: 3.821A  pdb=" N   LEU B 543 " --> pdb=" O   THR B 539 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLN B 552 " --> pdb=" O   VAL B 548 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ASN B 553 " --> pdb=" O   ALA B 549 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   VAL B 554 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   VAL B 555 " --> pdb=" O   LEU B 551 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1305 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: 1.59

  Time building geometry restraints manager: 1.70 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: 1836
        1.34 -     1.46: 1131
        1.46 -     1.57: 3001
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 6016
  Sorted by residual:
  bond pdb=" CA  SER B 536 "
       pdb=" C   SER B 536 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.015 1.72e-02 3.38e+03 7.56e-01
  bond pdb=" CA  SER A 536 "
       pdb=" C   SER A 536 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.015 1.72e-02 3.38e+03 7.56e-01
  bond pdb=" CG  LYS A 259 "
       pdb=" CD  LYS A 259 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.72e-01
  bond pdb=" CG  LYS B 259 "
       pdb=" CD  LYS B 259 "
    ideal  model  delta    sigma   weight residual
    1.520  1.542 -0.022 3.00e-02 1.11e+03 5.55e-01
  bond pdb=" CB  ILE A 209 "
       pdb=" CG2 ILE A 209 "
    ideal  model  delta    sigma   weight residual
    1.521  1.497  0.024 3.30e-02 9.18e+02 5.13e-01
  ... (remaining 6011 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 7839
        1.40 -     2.81: 258
        2.81 -     4.21: 41
        4.21 -     5.62: 9
        5.62 -     7.02: 5
  Bond angle restraints: 8152
  Sorted by residual:
  angle pdb=" N   VAL B 222 "
        pdb=" CA  VAL B 222 "
        pdb=" C   VAL B 222 "
      ideal   model   delta    sigma   weight residual
     113.53  108.68    4.85 9.80e-01 1.04e+00 2.45e+01
  angle pdb=" N   VAL A 222 "
        pdb=" CA  VAL A 222 "
        pdb=" C   VAL A 222 "
      ideal   model   delta    sigma   weight residual
     113.53  108.72    4.81 9.80e-01 1.04e+00 2.41e+01
  angle pdb=" N   PHE A 181 "
        pdb=" CA  PHE A 181 "
        pdb=" C   PHE A 181 "
      ideal   model   delta    sigma   weight residual
     111.02  105.13    5.89 1.22e+00 6.72e-01 2.33e+01
  angle pdb=" N   PHE B 181 "
        pdb=" CA  PHE B 181 "
        pdb=" C   PHE B 181 "
      ideal   model   delta    sigma   weight residual
     110.97  105.87    5.10 1.09e+00 8.42e-01 2.19e+01
  angle pdb=" N   LYS A 336 "
        pdb=" CA  LYS A 336 "
        pdb=" C   LYS A 336 "
      ideal   model   delta    sigma   weight residual
     114.31  108.36    5.95 1.29e+00 6.01e-01 2.13e+01
  ... (remaining 8147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3148
       17.01 -    34.01: 315
       34.01 -    51.02: 59
       51.02 -    68.02: 8
       68.02 -    85.03: 6
  Dihedral angle restraints: 3536
    sinusoidal: 1312
      harmonic: 2224
  Sorted by residual:
  dihedral pdb=" CA  MET A 398 "
           pdb=" C   MET A 398 "
           pdb=" N   GLU A 399 "
           pdb=" CA  GLU A 399 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.86  -18.14     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  MET B 398 "
           pdb=" C   MET B 398 "
           pdb=" N   GLU B 399 "
           pdb=" CA  GLU B 399 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.89  -18.11     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  GLU A 130 "
           pdb=" C   GLU A 130 "
           pdb=" N   PHE A 131 "
           pdb=" CA  PHE A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.44  -16.56     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 3533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 717
       0.043 -    0.085: 201
       0.085 -    0.128: 23
       0.128 -    0.170: 0
       0.170 -    0.213: 1
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" CA  LEU B 182 "
            pdb=" N   LEU B 182 "
            pdb=" C   LEU B 182 "
            pdb=" CB  LEU B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ILE A 363 "
            pdb=" N   ILE A 363 "
            pdb=" C   ILE A 363 "
            pdb=" CB  ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE B 363 "
            pdb=" N   ILE B 363 "
            pdb=" C   ILE B 363 "
            pdb=" CB  ILE B 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.60e-01
  ... (remaining 939 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 245 "   -0.022 5.00e-02 4.00e+02   3.39e-02 1.83e+00
        pdb=" N   PRO A 246 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 246 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 246 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 245 "   -0.022 5.00e-02 4.00e+02   3.37e-02 1.82e+00
        pdb=" N   PRO B 246 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO B 246 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 246 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 323 "    0.019 5.00e-02 4.00e+02   2.80e-02 1.25e+00
        pdb=" N   PRO B 324 "   -0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO B 324 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO B 324 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 899
        2.75 -     3.28: 6367
        3.28 -     3.82: 9940
        3.82 -     4.36: 11089
        4.36 -     4.90: 18345
  Nonbonded interactions: 46640
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 418 "
            pdb=" N   ALA B 532 "
     model   vdw
     2.208 3.200
  nonbonded pdb=" N   ALA A 532 "
            pdb=" NE2 GLN B 418 "
     model   vdw
     2.211 3.200
  nonbonded pdb=" O   PHE A 181 "
            pdb=" OG  SER B  91 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" NZ  LYS B 400 "
            pdb=" O   ALA B 565 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" NZ  LYS A 400 "
            pdb=" O   ALA A 565 "
     model   vdw
     2.218 3.120
  ... (remaining 46635 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.400
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
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      :  0.004   0.024   6016  Z= 0.168
  Angle     :  0.602   7.025   8152  Z= 0.358
  Chirality :  0.038   0.213    942
  Planarity :  0.003   0.034   1012
  Dihedral  : 14.302  85.025   2104
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 17.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.33), residues: 752
  helix:  0.78 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop : -2.36 (0.55), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 335 
 HIS   0.006   0.001   HIS A 254 
 PHE   0.012   0.001   PHE A 318 
 TYR   0.012   0.001   TYR A 299 
 ARG   0.010   0.001   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21417 (  435)
  hydrogen bonds       : angle       7.37813 ( 1305)
  covalent geometry    : bond        0.00362 ( 6016)
  covalent geometry    : angle       0.60169 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.9119 (mt) cc_final: 0.8836 (mt)
REVERT: A  259 LYS cc_start: 0.8871 (tppt) cc_final: 0.8561 (tptt)
REVERT: A  353 MET cc_start: 0.8684 (tpt) cc_final: 0.8451 (tpt)
REVERT: A  556 ASP cc_start: 0.8368 (m-30) cc_final: 0.8055 (m-30)
REVERT: A  563 GLN cc_start: 0.8441 (pp30) cc_final: 0.8023 (pp30)
REVERT: B  104 LEU cc_start: 0.9096 (mt) cc_final: 0.8811 (mt)
REVERT: B  259 LYS cc_start: 0.8870 (tppt) cc_final: 0.8560 (tptt)
REVERT: B  353 MET cc_start: 0.8684 (tpt) cc_final: 0.8450 (tpt)
REVERT: B  556 ASP cc_start: 0.8390 (m-30) cc_final: 0.8088 (m-30)
REVERT: B  563 GLN cc_start: 0.8434 (pp30) cc_final: 0.8021 (pp30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1524
  time to fit residues: 24.2876
Evaluate side-chains
  92 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 332 ASN
B 241 ASN
B 332 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.117798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.102450 restraints weight = 17497.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.105646 restraints weight = 14234.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.107551 restraints weight = 7105.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6016  Z= 0.150
  Angle     :  0.593   4.921   8152  Z= 0.324
  Chirality :  0.037   0.138    942
  Planarity :  0.004   0.032   1012
  Dihedral  :  4.511  14.616    816
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 10.80 %
    Favored  : 87.38 %
  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:  0.56 (0.32), residues: 752
  helix:  1.19 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.13 (0.51), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 120 
 HIS   0.005   0.002   HIS B 347 
 PHE   0.019   0.001   PHE B 177 
 TYR   0.038   0.002   TYR B 299 
 ARG   0.003   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04851 (  435)
  hydrogen bonds       : angle       4.40532 ( 1305)
  covalent geometry    : bond        0.00318 ( 6016)
  covalent geometry    : angle       0.59311 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8961 (mt) cc_final: 0.8705 (mt)
REVERT: A  255 ASN cc_start: 0.8964 (m-40) cc_final: 0.8762 (m-40)
REVERT: A  259 LYS cc_start: 0.8631 (tppt) cc_final: 0.8263 (ttmm)
REVERT: A  338 TYR cc_start: 0.8828 (m-80) cc_final: 0.8093 (m-80)
REVERT: A  353 MET cc_start: 0.8831 (tpt) cc_final: 0.8485 (tpt)
REVERT: A  391 LEU cc_start: 0.9036 (tp) cc_final: 0.8763 (tp)
REVERT: A  418 GLN cc_start: 0.9179 (tp40) cc_final: 0.8897 (tp40)
REVERT: A  546 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: A  556 ASP cc_start: 0.8304 (m-30) cc_final: 0.8104 (m-30)
REVERT: B  104 LEU cc_start: 0.8975 (mt) cc_final: 0.8715 (mt)
REVERT: B  255 ASN cc_start: 0.8980 (m-40) cc_final: 0.8775 (m-40)
REVERT: B  259 LYS cc_start: 0.8640 (tppt) cc_final: 0.8267 (ttmm)
REVERT: B  338 TYR cc_start: 0.8828 (m-80) cc_final: 0.8100 (m-80)
REVERT: B  353 MET cc_start: 0.8844 (tpt) cc_final: 0.8494 (tpt)
REVERT: B  391 LEU cc_start: 0.9024 (tp) cc_final: 0.8747 (tp)
REVERT: B  546 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7638 (tm-30)
REVERT: B  556 ASP cc_start: 0.8290 (m-30) cc_final: 0.8086 (m-30)
  outliers start: 11
  outliers final: 3
  residues processed: 104
  average time/residue: 0.1257
  time to fit residues: 18.8405
Evaluate side-chains
  90 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.102377 restraints weight = 17532.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.105712 restraints weight = 14202.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.107238 restraints weight = 7068.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6016  Z= 0.160
  Angle     :  0.559   4.915   8152  Z= 0.306
  Chirality :  0.038   0.154    942
  Planarity :  0.004   0.034   1012
  Dihedral  :  4.355  15.167    816
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 15.95 %
    Favored  : 83.06 %
  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:  0.84 (0.32), residues: 752
  helix:  1.40 (0.21), residues: 614
  sheet:  None (None), residues: 0
  loop : -3.41 (0.53), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.015   0.001   PHE B 181 
 TYR   0.030   0.001   TYR A 299 
 ARG   0.004   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04390 (  435)
  hydrogen bonds       : angle       4.24878 ( 1305)
  covalent geometry    : bond        0.00346 ( 6016)
  covalent geometry    : angle       0.55860 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.719 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8954 (mt) cc_final: 0.8708 (mt)
REVERT: A  181 PHE cc_start: 0.8508 (t80) cc_final: 0.8301 (t80)
REVERT: A  259 LYS cc_start: 0.8540 (tppt) cc_final: 0.8208 (ttmm)
REVERT: A  302 TYR cc_start: 0.6466 (p90) cc_final: 0.6170 (p90)
REVERT: A  338 TYR cc_start: 0.8797 (m-80) cc_final: 0.8113 (m-80)
REVERT: A  353 MET cc_start: 0.8666 (tpt) cc_final: 0.8154 (tpt)
REVERT: A  418 GLN cc_start: 0.9211 (tp40) cc_final: 0.9006 (tp40)
REVERT: A  546 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7440 (tm-30)
REVERT: A  556 ASP cc_start: 0.8094 (m-30) cc_final: 0.7880 (m-30)
REVERT: B  104 LEU cc_start: 0.8953 (mt) cc_final: 0.8707 (mt)
REVERT: B  259 LYS cc_start: 0.8556 (tppt) cc_final: 0.8201 (ttmm)
REVERT: B  302 TYR cc_start: 0.6517 (p90) cc_final: 0.6221 (p90)
REVERT: B  338 TYR cc_start: 0.8814 (m-80) cc_final: 0.8060 (m-80)
REVERT: B  353 MET cc_start: 0.8671 (tpt) cc_final: 0.8159 (tpt)
REVERT: B  418 GLN cc_start: 0.9208 (tp40) cc_final: 0.8993 (tp40)
REVERT: B  556 ASP cc_start: 0.8090 (m-30) cc_final: 0.7882 (m-30)
  outliers start: 6
  outliers final: 4
  residues processed: 102
  average time/residue: 0.1384
  time to fit residues: 19.9986
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 93
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  155 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 12 optimal weight:    7.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.118285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.103208 restraints weight = 17439.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.106495 restraints weight = 14208.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.108179 restraints weight = 7122.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.2869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6016  Z= 0.140
  Angle     :  0.527   5.658   8152  Z= 0.289
  Chirality :  0.037   0.159    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.213  14.490    816
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 18.60 %
    Favored  : 79.90 %
  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:  1.04 (0.32), residues: 752
  helix:  1.53 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.12 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 335 
 HIS   0.004   0.001   HIS A 254 
 PHE   0.014   0.001   PHE B 181 
 TYR   0.012   0.001   TYR A 275 
 ARG   0.003   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  435)
  hydrogen bonds       : angle       4.07134 ( 1305)
  covalent geometry    : bond        0.00301 ( 6016)
  covalent geometry    : angle       0.52742 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.643 
Fit side-chains
REVERT: A  255 ASN cc_start: 0.8817 (m-40) cc_final: 0.8567 (m-40)
REVERT: A  259 LYS cc_start: 0.8539 (tppt) cc_final: 0.8209 (ttmm)
REVERT: A  338 TYR cc_start: 0.8840 (m-80) cc_final: 0.8182 (m-80)
REVERT: A  353 MET cc_start: 0.8700 (tpt) cc_final: 0.8404 (tpt)
REVERT: A  418 GLN cc_start: 0.9247 (tp40) cc_final: 0.8978 (tp40)
REVERT: A  556 ASP cc_start: 0.8030 (m-30) cc_final: 0.7803 (m-30)
REVERT: B  104 LEU cc_start: 0.8934 (mt) cc_final: 0.8688 (mt)
REVERT: B  255 ASN cc_start: 0.8818 (m-40) cc_final: 0.8566 (m-40)
REVERT: B  259 LYS cc_start: 0.8549 (tppt) cc_final: 0.8206 (ttmm)
REVERT: B  338 TYR cc_start: 0.8839 (m-80) cc_final: 0.8172 (m-80)
REVERT: B  353 MET cc_start: 0.8690 (tpt) cc_final: 0.8395 (tpt)
REVERT: B  418 GLN cc_start: 0.9253 (tp40) cc_final: 0.8990 (tp40)
REVERT: B  556 ASP cc_start: 0.8029 (m-30) cc_final: 0.7802 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1211
  time to fit residues: 17.7589
Evaluate side-chains
  95 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.119921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.104855 restraints weight = 17134.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.108334 restraints weight = 14438.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.110027 restraints weight = 7059.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6016  Z= 0.119
  Angle     :  0.526   6.608   8152  Z= 0.283
  Chirality :  0.037   0.162    942
  Planarity :  0.003   0.036   1012
  Dihedral  :  4.054  14.239    816
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.76 %
    Favored  : 77.08 %
  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:  1.21 (0.33), residues: 752
  helix:  1.64 (0.22), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.05 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.003   0.001   HIS B 254 
 PHE   0.024   0.001   PHE A 227 
 TYR   0.029   0.001   TYR A 299 
 ARG   0.003   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03701 (  435)
  hydrogen bonds       : angle       3.91349 ( 1305)
  covalent geometry    : bond        0.00255 ( 6016)
  covalent geometry    : angle       0.52582 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.647 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8839 (mt) cc_final: 0.8612 (mt)
REVERT: A  157 MET cc_start: 0.7947 (mmt) cc_final: 0.7736 (mmm)
REVERT: A  259 LYS cc_start: 0.8452 (tppt) cc_final: 0.8245 (ttmm)
REVERT: A  338 TYR cc_start: 0.8799 (m-80) cc_final: 0.8271 (m-80)
REVERT: A  353 MET cc_start: 0.8647 (tpt) cc_final: 0.8437 (tpt)
REVERT: A  418 GLN cc_start: 0.9259 (tp40) cc_final: 0.8950 (tp40)
REVERT: B  104 LEU cc_start: 0.8897 (mt) cc_final: 0.8674 (mt)
REVERT: B  338 TYR cc_start: 0.8800 (m-80) cc_final: 0.8262 (m-80)
REVERT: B  353 MET cc_start: 0.8647 (tpt) cc_final: 0.8441 (tpt)
REVERT: B  418 GLN cc_start: 0.9260 (tp40) cc_final: 0.8956 (tp40)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1219
  time to fit residues: 18.0476
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 47 optimal weight:    0.0270
   chunk 27 optimal weight:    5.9990
   chunk 41 optimal weight:    0.4980
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 50 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.9442

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.119812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.104531 restraints weight = 17276.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.107935 restraints weight = 14149.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.109723 restraints weight = 7102.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6016  Z= 0.129
  Angle     :  0.549   7.362   8152  Z= 0.291
  Chirality :  0.037   0.168    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.020  14.022    816
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 22.59 %
    Favored  : 75.42 %
  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:  1.24 (0.32), residues: 752
  helix:  1.66 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.00 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 335 
 HIS   0.003   0.001   HIS B 254 
 PHE   0.012   0.001   PHE A 181 
 TYR   0.028   0.001   TYR A 299 
 ARG   0.003   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03725 (  435)
  hydrogen bonds       : angle       3.95393 ( 1305)
  covalent geometry    : bond        0.00282 ( 6016)
  covalent geometry    : angle       0.54887 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.729 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.8474 (tppt) cc_final: 0.8188 (ttmm)
REVERT: A  338 TYR cc_start: 0.8847 (m-80) cc_final: 0.8335 (m-80)
REVERT: A  353 MET cc_start: 0.8629 (tpt) cc_final: 0.8410 (tpt)
REVERT: A  418 GLN cc_start: 0.9267 (tp40) cc_final: 0.8968 (tp40)
REVERT: B  104 LEU cc_start: 0.8948 (mt) cc_final: 0.8718 (mt)
REVERT: B  338 TYR cc_start: 0.8838 (m-80) cc_final: 0.8269 (m-80)
REVERT: B  353 MET cc_start: 0.8648 (tpt) cc_final: 0.8424 (tpt)
REVERT: B  418 GLN cc_start: 0.9273 (tp40) cc_final: 0.8980 (tp40)
  outliers start: 12
  outliers final: 9
  residues processed: 100
  average time/residue: 0.1303
  time to fit residues: 18.9019
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.118478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.103098 restraints weight = 17347.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.106430 restraints weight = 14243.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.108200 restraints weight = 7139.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6016  Z= 0.150
  Angle     :  0.594   8.604   8152  Z= 0.310
  Chirality :  0.038   0.175    942
  Planarity :  0.004   0.035   1012
  Dihedral  :  4.067  14.569    816
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 23.92 %
    Favored  : 74.58 %
  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:  1.18 (0.32), residues: 752
  helix:  1.62 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.03 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.010   0.001   PHE A 181 
 TYR   0.007   0.001   TYR B 189 
 ARG   0.004   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03884 (  435)
  hydrogen bonds       : angle       4.06310 ( 1305)
  covalent geometry    : bond        0.00329 ( 6016)
  covalent geometry    : angle       0.59433 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  259 LYS cc_start: 0.8487 (tppt) cc_final: 0.8275 (ttmm)
REVERT: A  338 TYR cc_start: 0.8894 (m-80) cc_final: 0.8360 (m-80)
REVERT: A  353 MET cc_start: 0.8622 (tpt) cc_final: 0.8354 (tpt)
REVERT: A  418 GLN cc_start: 0.9240 (tp40) cc_final: 0.8951 (tp40)
REVERT: B  104 LEU cc_start: 0.8977 (mt) cc_final: 0.8749 (mt)
REVERT: B  338 TYR cc_start: 0.8874 (m-80) cc_final: 0.8326 (m-80)
REVERT: B  353 MET cc_start: 0.8631 (tpt) cc_final: 0.8363 (tpt)
REVERT: B  418 GLN cc_start: 0.9242 (tp40) cc_final: 0.8953 (tp40)
  outliers start: 9
  outliers final: 9
  residues processed: 96
  average time/residue: 0.1282
  time to fit residues: 17.8941
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    1.3384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.118390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.102995 restraints weight = 17183.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.106271 restraints weight = 14158.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.107998 restraints weight = 7209.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6016  Z= 0.154
  Angle     :  0.608   9.610   8152  Z= 0.318
  Chirality :  0.039   0.179    942
  Planarity :  0.004   0.035   1012
  Dihedral  :  4.121  14.705    816
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 24.09 %
    Favored  : 74.42 %
  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:  1.10 (0.32), residues: 752
  helix:  1.57 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.02 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 335 
 HIS   0.003   0.001   HIS B 254 
 PHE   0.032   0.001   PHE B 227 
 TYR   0.031   0.001   TYR B 299 
 ARG   0.004   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03918 (  435)
  hydrogen bonds       : angle       4.13584 ( 1305)
  covalent geometry    : bond        0.00337 ( 6016)
  covalent geometry    : angle       0.60827 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 0.681 
Fit side-chains
REVERT: A  338 TYR cc_start: 0.8903 (m-80) cc_final: 0.8332 (m-80)
REVERT: A  353 MET cc_start: 0.8618 (tpt) cc_final: 0.8335 (tpt)
REVERT: A  418 GLN cc_start: 0.9232 (tp40) cc_final: 0.8935 (tp40)
REVERT: B  104 LEU cc_start: 0.8951 (mt) cc_final: 0.8693 (mt)
REVERT: B  338 TYR cc_start: 0.8893 (m-80) cc_final: 0.8317 (m-80)
REVERT: B  353 MET cc_start: 0.8625 (tpt) cc_final: 0.8337 (tpt)
REVERT: B  418 GLN cc_start: 0.9244 (tp40) cc_final: 0.8950 (tp40)
  outliers start: 9
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1229
  time to fit residues: 17.7258
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.119994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.104670 restraints weight = 17159.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.108058 restraints weight = 14471.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.109941 restraints weight = 7195.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6016  Z= 0.131
  Angle     :  0.617  10.377   8152  Z= 0.319
  Chirality :  0.038   0.181    942
  Planarity :  0.003   0.036   1012
  Dihedral  :  4.060  14.546    816
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 23.75 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.32), residues: 752
  helix:  1.61 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.81 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.035   0.001   PHE A 227 
 TYR   0.006   0.001   TYR A 302 
 ARG   0.003   0.000   ARG B 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  435)
  hydrogen bonds       : angle       4.05548 ( 1305)
  covalent geometry    : bond        0.00283 ( 6016)
  covalent geometry    : angle       0.61726 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  181 PHE cc_start: 0.8401 (t80) cc_final: 0.8168 (t80)
REVERT: A  338 TYR cc_start: 0.8850 (m-80) cc_final: 0.8325 (m-80)
REVERT: A  353 MET cc_start: 0.8598 (tpt) cc_final: 0.8363 (tpt)
REVERT: A  418 GLN cc_start: 0.9212 (tp40) cc_final: 0.8867 (tp40)
REVERT: B  104 LEU cc_start: 0.8918 (mt) cc_final: 0.8694 (mt)
REVERT: B  338 TYR cc_start: 0.8839 (m-80) cc_final: 0.8298 (m-80)
REVERT: B  353 MET cc_start: 0.8601 (tpt) cc_final: 0.8366 (tpt)
REVERT: B  418 GLN cc_start: 0.9241 (tp40) cc_final: 0.8895 (tp40)
  outliers start: 9
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1203
  time to fit residues: 17.9511
Evaluate side-chains
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0470
   chunk 67 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.121508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.106196 restraints weight = 17123.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.109639 restraints weight = 14121.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.111505 restraints weight = 7074.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6016  Z= 0.122
  Angle     :  0.640  11.394   8152  Z= 0.321
  Chirality :  0.038   0.181    942
  Planarity :  0.003   0.036   1012
  Dihedral  :  3.958  13.892    816
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 25.42 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.33), residues: 752
  helix:  1.79 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.54 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 335 
 HIS   0.004   0.001   HIS B 254 
 PHE   0.016   0.001   PHE B 227 
 TYR   0.030   0.001   TYR B 299 
 ARG   0.003   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03542 (  435)
  hydrogen bonds       : angle       3.96463 ( 1305)
  covalent geometry    : bond        0.00263 ( 6016)
  covalent geometry    : angle       0.64048 ( 8152)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  338 TYR cc_start: 0.8866 (m-80) cc_final: 0.8344 (m-80)
REVERT: A  353 MET cc_start: 0.8588 (tpt) cc_final: 0.8357 (tpt)
REVERT: A  418 GLN cc_start: 0.9237 (tp40) cc_final: 0.8883 (tp40)
REVERT: B  104 LEU cc_start: 0.8926 (mt) cc_final: 0.8692 (mt)
REVERT: B  338 TYR cc_start: 0.8846 (m-80) cc_final: 0.8329 (m-80)
REVERT: B  353 MET cc_start: 0.8598 (tpt) cc_final: 0.8357 (tpt)
REVERT: B  418 GLN cc_start: 0.9241 (tp40) cc_final: 0.8895 (tp40)
  outliers start: 8
  outliers final: 6
  residues processed: 107
  average time/residue: 0.1355
  time to fit residues: 20.9057
Evaluate side-chains
  102 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Chi-restraints excluded: chain B residue  406 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0170
   chunk 71 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.121637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.106245 restraints weight = 17193.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.109654 restraints weight = 14264.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.111535 restraints weight = 7179.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6016  Z= 0.122
  Angle     :  0.640  10.579   8152  Z= 0.320
  Chirality :  0.038   0.183    942
  Planarity :  0.003   0.036   1012
  Dihedral  :  3.931  13.646    816
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 25.25 %
    Favored  : 73.92 %
  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:  1.52 (0.33), residues: 752
  helix:  1.83 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.36 (0.58), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.017   0.001   PHE B 227 
 TYR   0.035   0.001   TYR A 275 
 ARG   0.003   0.000   ARG A 550 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03558 (  435)
  hydrogen bonds       : angle       3.91688 ( 1305)
  covalent geometry    : bond        0.00261 ( 6016)
  covalent geometry    : angle       0.63965 ( 8152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1765.26 seconds
wall clock time: 31 minutes 36.47 seconds (1896.47 seconds total)