Starting phenix.real_space_refine
on Tue Feb 11 13:51:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hiy_34829/02_2025/8hiy_34829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hiy_34829/02_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_34829/02_2025/8hiy_34829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hiy_34829/02_2025/8hiy_34829.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hiy_34829/02_2025/8hiy_34829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hiy_34829/02_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-5592/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: 5.11, per 1000 atoms: 0.87
  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: 1.51
  Conformation dependent library (CDL) restraints added in 727.8 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: 0.80
  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: 1.75

  Time building geometry restraints manager: 1.75 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:             1.950
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.420
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.080
-------------------------------------------------------------------------------
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= 0.232
  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 

*********************** 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  : 0.625 
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: 0.1569
  time to fit residues: 24.9737
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  : 0.717 
-------------------------------------------------------------------------------
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 = 17497.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.105645 restraints weight = 14233.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.107578 restraints weight = 7105.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
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= 0.206
  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 

*********************** 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  : 0.681 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8962 (mt) cc_final: 0.8706 (mt)
REVERT: A  255 ASN cc_start: 0.8964 (m-40) cc_final: 0.8763 (m-40)
REVERT: A  259 LYS cc_start: 0.8630 (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: 0.9037 (tp) cc_final: 0.8763 (tp)
REVERT: A  418 GLN cc_start: 0.9178 (tp40) cc_final: 0.8897 (tp40)
REVERT: A  546 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7648 (tm-30)
REVERT: A  556 ASP cc_start: 0.8306 (m-30) cc_final: 0.8105 (m-30)
REVERT: B  104 LEU cc_start: 0.8977 (mt) cc_final: 0.8716 (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: 0.8266 (ttmm)
REVERT: B  338 TYR cc_start: 0.8828 (m-80) cc_final: 0.8101 (m-80)
REVERT: B  353 MET cc_start: 0.8845 (tpt) cc_final: 0.8495 (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: 0.8292 (m-30) cc_final: 0.8088 (m-30)
  outliers start: 11
  outliers final: 3
  residues processed: 104
  average time/residue: 0.1336
  time to fit residues: 19.9330
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  : 0.783 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.117012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.101975 restraints weight = 17562.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.105280 restraints weight = 14392.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.106919 restraints weight = 7117.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6016  Z= 0.231
  Angle     :  0.565   5.178   8152  Z= 0.310
  Chirality :  0.038   0.156    942
  Planarity :  0.004   0.034   1012
  Dihedral  :  4.382  15.415    816
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 16.11 %
    Favored  : 82.72 %
  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:  0.83 (0.32), residues: 752
  helix:  1.40 (0.21), residues: 612
  sheet:  None (None), residues: 0
  loop : -3.36 (0.52), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.014   0.001   PHE B 227 
 TYR   0.030   0.001   TYR B 299 
 ARG   0.004   0.000   ARG B 550 

*********************** 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
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8965 (mt) cc_final: 0.8699 (mt)
REVERT: A  259 LYS cc_start: 0.8556 (tppt) cc_final: 0.8212 (ttmm)
REVERT: A  338 TYR cc_start: 0.8799 (m-80) cc_final: 0.8109 (m-80)
REVERT: A  353 MET cc_start: 0.8664 (tpt) cc_final: 0.8377 (tpt)
REVERT: A  546 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7442 (tm-30)
REVERT: A  556 ASP cc_start: 0.8111 (m-30) cc_final: 0.7893 (m-30)
REVERT: B  104 LEU cc_start: 0.8961 (mt) cc_final: 0.8695 (mt)
REVERT: B  181 PHE cc_start: 0.8472 (t80) cc_final: 0.8157 (t80)
REVERT: B  259 LYS cc_start: 0.8577 (tppt) cc_final: 0.8233 (ttmm)
REVERT: B  338 TYR cc_start: 0.8812 (m-80) cc_final: 0.8105 (m-80)
REVERT: B  353 MET cc_start: 0.8675 (tpt) cc_final: 0.8378 (tpt)
REVERT: B  418 GLN cc_start: 0.9198 (tp40) cc_final: 0.8994 (tp40)
REVERT: B  546 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7451 (tm-30)
REVERT: B  556 ASP cc_start: 0.8112 (m-30) cc_final: 0.7895 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1516
  time to fit residues: 21.1602
Evaluate side-chains
  100 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  155 LEU
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:    0.8980
   chunk 52 optimal weight:    0.0770
   chunk 12 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    0.9540

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.118881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103846 restraints weight = 17458.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.107200 restraints weight = 14327.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.109113 restraints weight = 7097.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2915

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= 0.181
  Angle     :  0.520   5.478   8152  Z= 0.285
  Chirality :  0.037   0.156    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.174  14.403    816
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 18.44 %
    Favored  : 80.07 %
  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:  1.17 (0.33), residues: 752
  helix:  1.59 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.84 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 335 
 HIS   0.004   0.001   HIS A 254 
 PHE   0.015   0.001   PHE B 181 
 TYR   0.011   0.001   TYR A 275 
 ARG   0.003   0.000   ARG B 550 

*********************** 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
  104 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8939 (mt) cc_final: 0.8686 (mt)
REVERT: A  255 ASN cc_start: 0.8793 (m-40) cc_final: 0.8547 (m-40)
REVERT: A  259 LYS cc_start: 0.8514 (tppt) cc_final: 0.8188 (ttmm)
REVERT: A  338 TYR cc_start: 0.8823 (m-80) cc_final: 0.8184 (m-80)
REVERT: A  353 MET cc_start: 0.8681 (tpt) cc_final: 0.8384 (tpt)
REVERT: A  418 GLN cc_start: 0.9349 (tp40) cc_final: 0.9072 (tp40)
REVERT: A  556 ASP cc_start: 0.8023 (m-30) cc_final: 0.7800 (m-30)
REVERT: B  104 LEU cc_start: 0.8927 (mt) cc_final: 0.8678 (mt)
REVERT: B  181 PHE cc_start: 0.8400 (t80) cc_final: 0.8181 (t80)
REVERT: B  255 ASN cc_start: 0.8797 (m-40) cc_final: 0.8552 (m-40)
REVERT: B  259 LYS cc_start: 0.8531 (tppt) cc_final: 0.8219 (ttmm)
REVERT: B  338 TYR cc_start: 0.8817 (m-80) cc_final: 0.8173 (m-80)
REVERT: B  353 MET cc_start: 0.8676 (tpt) cc_final: 0.8383 (tpt)
REVERT: B  418 GLN cc_start: 0.9236 (tp40) cc_final: 0.8954 (tp40)
REVERT: B  556 ASP cc_start: 0.8022 (m-30) cc_final: 0.7796 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.1411
  time to fit residues: 20.4956
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.119287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.104026 restraints weight = 17266.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.107435 restraints weight = 14203.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.109224 restraints weight = 7028.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3221

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= 0.173
  Angle     :  0.525   6.346   8152  Z= 0.283
  Chirality :  0.037   0.163    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.061  14.183    816
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.43 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.33), residues: 752
  helix:  1.66 (0.22), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.88 (0.54), 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   0.016   0.001   PHE A 181 
 TYR   0.028   0.001   TYR B 299 
 ARG   0.003   0.000   ARG B 550 

*********************** 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
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.670 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8946 (mt) cc_final: 0.8715 (mt)
REVERT: A  157 MET cc_start: 0.8020 (mmt) cc_final: 0.7797 (mmm)
REVERT: A  338 TYR cc_start: 0.8856 (m-80) cc_final: 0.8293 (m-80)
REVERT: A  353 MET cc_start: 0.8681 (tpt) cc_final: 0.8470 (tpt)
REVERT: A  556 ASP cc_start: 0.8018 (m-30) cc_final: 0.7803 (m-30)
REVERT: B  104 LEU cc_start: 0.8950 (mt) cc_final: 0.8721 (mt)
REVERT: B  157 MET cc_start: 0.8042 (mmt) cc_final: 0.7820 (mmm)
REVERT: B  181 PHE cc_start: 0.8447 (t80) cc_final: 0.8238 (t80)
REVERT: B  338 TYR cc_start: 0.8854 (m-80) cc_final: 0.8286 (m-80)
REVERT: B  353 MET cc_start: 0.8682 (tpt) cc_final: 0.8471 (tpt)
REVERT: B  418 GLN cc_start: 0.9265 (tp40) cc_final: 0.8998 (tp40)
REVERT: B  556 ASP cc_start: 0.8036 (m-30) cc_final: 0.7819 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1353
  time to fit residues: 19.8966
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  : 0.760 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 25 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    0.8788

-------------------------------------------------------------------------------
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 = 0.3803 r_free = 0.3803 target = 0.119822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.104547 restraints weight = 17331.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.107775 restraints weight = 14443.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.109780 restraints weight = 7284.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6016  Z= 0.179
  Angle     :  0.547   7.315   8152  Z= 0.288
  Chirality :  0.037   0.170    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.005  14.117    816
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 21.59 %
    Favored  : 76.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.32), residues: 752
  helix:  1.66 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -2.94 (0.53), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 335 
 HIS   0.003   0.001   HIS B 254 
 PHE   0.014   0.001   PHE B 181 
 TYR   0.007   0.001   TYR A 275 
 ARG   0.003   0.000   ARG B 550 

*********************** 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
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8951 (mt) cc_final: 0.8719 (mt)
REVERT: A  338 TYR cc_start: 0.8837 (m-80) cc_final: 0.8270 (m-80)
REVERT: A  353 MET cc_start: 0.8655 (tpt) cc_final: 0.8415 (tpt)
REVERT: A  556 ASP cc_start: 0.8008 (m-30) cc_final: 0.7796 (m-30)
REVERT: B  104 LEU cc_start: 0.8942 (mt) cc_final: 0.8710 (mt)
REVERT: B  338 TYR cc_start: 0.8834 (m-80) cc_final: 0.8260 (m-80)
REVERT: B  353 MET cc_start: 0.8657 (tpt) cc_final: 0.8416 (tpt)
REVERT: B  418 GLN cc_start: 0.9272 (tp40) cc_final: 0.8971 (tp40)
REVERT: B  556 ASP cc_start: 0.7996 (m-30) cc_final: 0.7764 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1273
  time to fit residues: 19.2062
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  : 0.684 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    9.9990
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3809 r_free = 0.3809 target = 0.120169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.104910 restraints weight = 17267.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.108323 restraints weight = 14604.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.110169 restraints weight = 7195.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3468

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= 0.182
  Angle     :  0.578   8.792   8152  Z= 0.299
  Chirality :  0.037   0.173    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.959  14.182    816
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 23.26 %
    Favored  : 75.25 %
  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:  1.29 (0.33), residues: 752
  helix:  1.71 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.93 (0.53), residues: 146

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   0.011   0.001   PHE A 227 
 TYR   0.030   0.001   TYR B 299 
 ARG   0.003   0.000   ARG B 550 

*********************** 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
  103 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8917 (mt) cc_final: 0.8689 (mt)
REVERT: A  338 TYR cc_start: 0.8813 (m-80) cc_final: 0.8325 (m-80)
REVERT: A  353 MET cc_start: 0.8613 (tpt) cc_final: 0.8393 (tpt)
REVERT: A  556 ASP cc_start: 0.7948 (m-30) cc_final: 0.7736 (m-30)
REVERT: B  104 LEU cc_start: 0.8916 (mt) cc_final: 0.8690 (mt)
REVERT: B  338 TYR cc_start: 0.8794 (m-80) cc_final: 0.8301 (m-80)
REVERT: B  353 MET cc_start: 0.8604 (tpt) cc_final: 0.8379 (tpt)
REVERT: B  418 GLN cc_start: 0.9239 (tp40) cc_final: 0.8916 (tp40)
REVERT: B  556 ASP cc_start: 0.7948 (m-30) cc_final: 0.7741 (m-30)
  outliers start: 9
  outliers final: 9
  residues processed: 99
  average time/residue: 0.1392
  time to fit residues: 19.6885
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  : 0.638 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 14 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3814 r_free = 0.3814 target = 0.120572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.105363 restraints weight = 17009.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.108625 restraints weight = 14098.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.110520 restraints weight = 7051.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6016  Z= 0.180
  Angle     :  0.579   9.352   8152  Z= 0.302
  Chirality :  0.038   0.176    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.996  14.230    816
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 23.42 %
    Favored  : 74.92 %
  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:  1.30 (0.32), residues: 752
  helix:  1.70 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.84 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.030   0.001   PHE B 227 
 TYR   0.007   0.001   TYR B 299 
 ARG   0.003   0.000   ARG B 550 

*********************** 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
  106 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.660 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8969 (mt) cc_final: 0.8733 (mt)
REVERT: A  338 TYR cc_start: 0.8875 (m-80) cc_final: 0.8322 (m-80)
REVERT: A  353 MET cc_start: 0.8630 (tpt) cc_final: 0.8393 (tpt)
REVERT: A  418 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.8893 (tp40)
REVERT: A  556 ASP cc_start: 0.7982 (m-30) cc_final: 0.7758 (m-30)
REVERT: B  104 LEU cc_start: 0.8956 (mt) cc_final: 0.8722 (mt)
REVERT: B  338 TYR cc_start: 0.8858 (m-80) cc_final: 0.8294 (m-80)
REVERT: B  353 MET cc_start: 0.8634 (tpt) cc_final: 0.8396 (tpt)
REVERT: B  418 GLN cc_start: 0.9247 (tp40) cc_final: 0.8931 (tp40)
REVERT: B  556 ASP cc_start: 0.7984 (m-30) cc_final: 0.7764 (m-30)
  outliers start: 10
  outliers final: 9
  residues processed: 101
  average time/residue: 0.1287
  time to fit residues: 18.7566
Evaluate side-chains
  107 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
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 A residue  418 GLN
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:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 42 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   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 = 0.3813 r_free = 0.3813 target = 0.120591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.105250 restraints weight = 17168.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.108608 restraints weight = 14143.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.110514 restraints weight = 7057.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3598

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= 0.181
  Angle     :  0.605  10.055   8152  Z= 0.313
  Chirality :  0.038   0.179    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  4.023  14.496    816
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 24.09 %
    Favored  : 74.25 %
  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:  1.33 (0.32), residues: 752
  helix:  1.70 (0.21), residues: 606
  sheet:  None (None), residues: 0
  loop : -2.74 (0.53), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.036   0.001   PHE A 227 
 TYR   0.031   0.001   TYR B 299 
 ARG   0.003   0.000   ARG A 550 

*********************** 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
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8971 (mt) cc_final: 0.8742 (mt)
REVERT: A  338 TYR cc_start: 0.8869 (m-80) cc_final: 0.8299 (m-80)
REVERT: A  353 MET cc_start: 0.8629 (tpt) cc_final: 0.8388 (tpt)
REVERT: A  418 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8773 (tp40)
REVERT: A  556 ASP cc_start: 0.7974 (m-30) cc_final: 0.7751 (m-30)
REVERT: B  104 LEU cc_start: 0.8967 (mt) cc_final: 0.8734 (mt)
REVERT: B  338 TYR cc_start: 0.8856 (m-80) cc_final: 0.8277 (m-80)
REVERT: B  353 MET cc_start: 0.8619 (tpt) cc_final: 0.8385 (tpt)
REVERT: B  418 GLN cc_start: 0.9244 (tp40) cc_final: 0.8926 (tp40)
REVERT: B  556 ASP cc_start: 0.7973 (m-30) cc_final: 0.7762 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 104
  average time/residue: 0.1323
  time to fit residues: 19.5979
Evaluate side-chains
  105 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
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 A residue  418 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0010
   chunk 5 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0870
   chunk 75 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4364

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

Flipped N/Q/H residues before XYZ refinement:
A 364 GLN
** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.122485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.107282 restraints weight = 17108.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.110668 restraints weight = 14533.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.112647 restraints weight = 7249.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6016  Z= 0.162
  Angle     :  0.635  11.450   8152  Z= 0.316
  Chirality :  0.038   0.181    942
  Planarity :  0.003   0.036   1012
  Dihedral  :  3.907  13.741    816
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 24.75 %
    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:  1.59 (0.33), residues: 752
  helix:  1.93 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -2.49 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 335 
 HIS   0.004   0.001   HIS A 254 
 PHE   0.018   0.001   PHE A 227 
 TYR   0.008   0.001   TYR A 302 
 ARG   0.002   0.000   ARG B 550 

********************** 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: 5
    poor density    : 106
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8918 (mt) cc_final: 0.8686 (mt)
REVERT: A  338 TYR cc_start: 0.8809 (m-80) cc_final: 0.8364 (m-80)
REVERT: A  353 MET cc_start: 0.8586 (tpt) cc_final: 0.8369 (tpt)
REVERT: B  104 LEU cc_start: 0.8922 (mt) cc_final: 0.8687 (mt)
REVERT: B  338 TYR cc_start: 0.8811 (m-80) cc_final: 0.8313 (m-80)
REVERT: B  353 MET cc_start: 0.8576 (tpt) cc_final: 0.8368 (tpt)
REVERT: B  418 GLN cc_start: 0.9237 (tp40) cc_final: 0.8922 (tp40)
  outliers start: 5
  outliers final: 3
  residues processed: 109
  average time/residue: 0.1250
  time to fit residues: 19.8233
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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**
B 364 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.121005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105714 restraints weight = 17291.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.109066 restraints weight = 14946.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.110976 restraints weight = 7397.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.3842

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= 0.186
  Angle     :  0.651  10.801   8152  Z= 0.332
  Chirality :  0.041   0.253    942
  Planarity :  0.004   0.035   1012
  Dihedral  :  3.932  13.723    816
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 26.25 %
    Favored  : 72.92 %
  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:  1.55 (0.33), residues: 752
  helix:  1.88 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -2.41 (0.57), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 
 PHE   0.041   0.001   PHE A 227 
 TYR   0.032   0.001   TYR B 299 
 ARG   0.003   0.000   ARG A 550 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1638.39 seconds
wall clock time: 30 minutes 38.23 seconds (1838.23 seconds total)