Starting phenix.real_space_refine
on Fri Aug 22 16:28:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hiy_34829/08_2025/8hiy_34829.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hiy_34829/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hiy_34829/08_2025/8hiy_34829.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hiy_34829/08_2025/8hiy_34829.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hiy_34829/08_2025/8hiy_34829.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hiy_34829/08_2025/8hiy_34829.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'PHE:plan': 3}
          Unresolved non-hydrogen planarities: 61
  Restraints were copied for chains:
    B
  Time building chain proxies: 1.85, per 1000 atoms: 0.31
  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: 0.39
  Conformation dependent library (CDL) restraints added in 208.9 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.09
  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: 0.77

  Time building geometry restraints manager: 0.55 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: 0.01
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:             1.540
  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:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.380
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.160
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG A 200 
 TYR   0.012   0.001   TYR A 299 
 PHE   0.012   0.001   PHE A 318 
 TRP   0.010   0.001   TRP A 335 
 HIS   0.006   0.001   HIS A 254 

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

*********************** 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  : 0.208 
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: 0.0499
  time to fit residues: 8.1428
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  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7078

-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.118610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103415 restraints weight = 17565.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.106613 restraints weight = 14493.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.108840 restraints weight = 7227.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.109137 restraints weight = 5196.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.109212 restraints weight = 4497.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6016  Z= 0.142
  Angle     :  0.583   4.857   8152  Z= 0.318
  Chirality :  0.037   0.136    942
  Planarity :  0.004   0.032   1012
  Dihedral  :  4.483  14.691    816
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 11.13 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.32), residues: 752
  helix:  1.22 (0.22), residues: 606
  sheet:  None (None), residues: 0
  loop : -3.13 (0.50), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 550 
 TYR   0.037   0.002   TYR B 299 
 PHE   0.020   0.001   PHE B 177 
 TRP   0.008   0.001   TRP A 120 
 HIS   0.005   0.002   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6016)
  covalent geometry    : angle       0.58282 ( 8152)
  hydrogen bonds       : bond        0.04817 (  435)
  hydrogen bonds       : angle       4.36184 ( 1305)

*********************** 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
  112 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.9021 (mt) cc_final: 0.8771 (mt)
REVERT: A  259 LYS cc_start: 0.8617 (tppt) cc_final: 0.8250 (ttmm)
REVERT: A  338 TYR cc_start: 0.8834 (m-80) cc_final: 0.8134 (m-80)
REVERT: A  353 MET cc_start: 0.8802 (tpt) cc_final: 0.8474 (tpt)
REVERT: A  391 LEU cc_start: 0.9017 (tp) cc_final: 0.8762 (tp)
REVERT: A  418 GLN cc_start: 0.9142 (tp40) cc_final: 0.8862 (tp40)
REVERT: A  556 ASP cc_start: 0.8295 (m-30) cc_final: 0.8092 (m-30)
REVERT: B  104 LEU cc_start: 0.9008 (mt) cc_final: 0.8769 (mt)
REVERT: B  259 LYS cc_start: 0.8622 (tppt) cc_final: 0.8249 (ttmm)
REVERT: B  338 TYR cc_start: 0.8805 (m-80) cc_final: 0.8198 (m-80)
REVERT: B  353 MET cc_start: 0.8810 (tpt) cc_final: 0.8479 (tpt)
REVERT: B  391 LEU cc_start: 0.9023 (tp) cc_final: 0.8766 (tp)
REVERT: B  418 GLN cc_start: 0.9139 (tp40) cc_final: 0.8859 (tp40)
REVERT: B  556 ASP cc_start: 0.8289 (m-30) cc_final: 0.8085 (m-30)
  outliers start: 11
  outliers final: 2
  residues processed: 106
  average time/residue: 0.0489
  time to fit residues: 7.6271
Evaluate side-chains
  89 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain B residue   99 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   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 = 0.3798 r_free = 0.3798 target = 0.119244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.104248 restraints weight = 17300.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.107622 restraints weight = 13535.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.109594 restraints weight = 6745.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.110241 restraints weight = 4903.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.110363 restraints weight = 4031.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.2797

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= 0.129
  Angle     :  0.540   5.363   8152  Z= 0.293
  Chirality :  0.037   0.155    942
  Planarity :  0.004   0.034   1012
  Dihedral  :  4.200  14.329    816
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 16.28 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.33), residues: 752
  helix:  1.50 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.15 (0.56), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 550 
 TYR   0.031   0.001   TYR A 299 
 PHE   0.015   0.001   PHE A 227 
 TRP   0.010   0.001   TRP A 335 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6016)
  covalent geometry    : angle       0.54011 ( 8152)
  hydrogen bonds       : bond        0.04095 (  435)
  hydrogen bonds       : angle       4.06469 ( 1305)

*********************** 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
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.9008 (mt) cc_final: 0.8748 (mt)
REVERT: A  181 PHE cc_start: 0.8433 (t80) cc_final: 0.8178 (t80)
REVERT: A  259 LYS cc_start: 0.8529 (tppt) cc_final: 0.8171 (ttmm)
REVERT: A  338 TYR cc_start: 0.8880 (m-80) cc_final: 0.8221 (m-80)
REVERT: A  353 MET cc_start: 0.8679 (tpt) cc_final: 0.8192 (tpt)
REVERT: A  418 GLN cc_start: 0.9214 (tp40) cc_final: 0.8978 (tp40)
REVERT: A  556 ASP cc_start: 0.8156 (m-30) cc_final: 0.7890 (m-30)
REVERT: B  104 LEU cc_start: 0.9018 (mt) cc_final: 0.8752 (mt)
REVERT: B  259 LYS cc_start: 0.8537 (tppt) cc_final: 0.8185 (ttmm)
REVERT: B  338 TYR cc_start: 0.8888 (m-80) cc_final: 0.8223 (m-80)
REVERT: B  353 MET cc_start: 0.8678 (tpt) cc_final: 0.8186 (tpt)
REVERT: B  418 GLN cc_start: 0.9211 (tp40) cc_final: 0.8978 (tp40)
REVERT: B  556 ASP cc_start: 0.8107 (m-30) cc_final: 0.7839 (m-30)
  outliers start: 3
  outliers final: 3
  residues processed: 101
  average time/residue: 0.0517
  time to fit residues: 7.7685
Evaluate side-chains
  93 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    6.9990
   chunk 2 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   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 = 0.3800 r_free = 0.3800 target = 0.119325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.104062 restraints weight = 17545.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.107426 restraints weight = 14193.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.109318 restraints weight = 7102.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.110076 restraints weight = 5225.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.110259 restraints weight = 4306.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3073

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= 0.125
  Angle     :  0.519   5.358   8152  Z= 0.282
  Chirality :  0.037   0.154    942
  Planarity :  0.003   0.034   1012
  Dihedral  :  4.068  13.977    816
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 18.60 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.32), residues: 752
  helix:  1.57 (0.21), residues: 610
  sheet:  None (None), residues: 0
  loop : -3.06 (0.55), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 550 
 TYR   0.026   0.001   TYR A 299 
 PHE   0.019   0.001   PHE B 177 
 TRP   0.006   0.001   TRP A 335 
 HIS   0.005   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6016)
  covalent geometry    : angle       0.51859 ( 8152)
  hydrogen bonds       : bond        0.03814 (  435)
  hydrogen bonds       : angle       3.91563 ( 1305)

*********************** 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
  98 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.9013 (mt) cc_final: 0.8726 (mt)
REVERT: A  181 PHE cc_start: 0.8453 (t80) cc_final: 0.8242 (t80)
REVERT: A  259 LYS cc_start: 0.8485 (tppt) cc_final: 0.8252 (ttmm)
REVERT: A  338 TYR cc_start: 0.8858 (m-80) cc_final: 0.8246 (m-80)
REVERT: A  353 MET cc_start: 0.8777 (tpt) cc_final: 0.8471 (tpt)
REVERT: A  418 GLN cc_start: 0.9223 (tp40) cc_final: 0.8935 (tp40)
REVERT: A  556 ASP cc_start: 0.8110 (m-30) cc_final: 0.7863 (m-30)
REVERT: B  104 LEU cc_start: 0.9019 (mt) cc_final: 0.8729 (mt)
REVERT: B  259 LYS cc_start: 0.8489 (tppt) cc_final: 0.8260 (ttmm)
REVERT: B  338 TYR cc_start: 0.8860 (m-80) cc_final: 0.8246 (m-80)
REVERT: B  353 MET cc_start: 0.8772 (tpt) cc_final: 0.8468 (tpt)
REVERT: B  418 GLN cc_start: 0.9226 (tp40) cc_final: 0.8949 (tp40)
REVERT: B  556 ASP cc_start: 0.8088 (m-30) cc_final: 0.7846 (m-30)
  outliers start: 5
  outliers final: 5
  residues processed: 96
  average time/residue: 0.0461
  time to fit residues: 6.5588
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0670
   chunk 62 optimal weight:    0.7980
   chunk 27 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.120778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.105673 restraints weight = 17595.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.109206 restraints weight = 14254.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.111026 restraints weight = 6970.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111850 restraints weight = 5133.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.112069 restraints weight = 4209.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6016  Z= 0.109
  Angle     :  0.515   6.843   8152  Z= 0.274
  Chirality :  0.036   0.160    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.927  14.195    816
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 19.77 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.33 (0.33), residues: 752
  helix:  1.71 (0.22), residues: 610
  sheet:  None (None), residues: 0
  loop : -2.91 (0.54), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 550 
 TYR   0.011   0.001   TYR B 302 
 PHE   0.035   0.001   PHE B 219 
 TRP   0.007   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 6016)
  covalent geometry    : angle       0.51518 ( 8152)
  hydrogen bonds       : bond        0.03553 (  435)
  hydrogen bonds       : angle       3.79124 ( 1305)

*********************** 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
  110 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.9008 (mt) cc_final: 0.8765 (mt)
REVERT: A  181 PHE cc_start: 0.8487 (t80) cc_final: 0.8281 (t80)
REVERT: A  259 LYS cc_start: 0.8450 (tppt) cc_final: 0.8138 (ttmm)
REVERT: A  338 TYR cc_start: 0.8839 (m-80) cc_final: 0.8280 (m-80)
REVERT: A  353 MET cc_start: 0.8681 (tpt) cc_final: 0.8428 (tpt)
REVERT: A  418 GLN cc_start: 0.9253 (tp40) cc_final: 0.8943 (tp40)
REVERT: A  556 ASP cc_start: 0.8058 (m-30) cc_final: 0.7820 (m-30)
REVERT: B  104 LEU cc_start: 0.9008 (mt) cc_final: 0.8768 (mt)
REVERT: B  259 LYS cc_start: 0.8452 (tppt) cc_final: 0.8130 (ttmm)
REVERT: B  338 TYR cc_start: 0.8842 (m-80) cc_final: 0.8282 (m-80)
REVERT: B  353 MET cc_start: 0.8682 (tpt) cc_final: 0.8426 (tpt)
REVERT: B  418 GLN cc_start: 0.9249 (tp40) cc_final: 0.8948 (tp40)
REVERT: B  556 ASP cc_start: 0.8036 (m-30) cc_final: 0.7803 (m-30)
  outliers start: 9
  outliers final: 3
  residues processed: 108
  average time/residue: 0.0533
  time to fit residues: 8.4713
Evaluate side-chains
  95 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 24 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   chunk 62 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0670
   chunk 12 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.6320

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
B 337 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.120872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.105743 restraints weight = 17532.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.109194 restraints weight = 14665.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.110971 restraints weight = 7233.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.111885 restraints weight = 5424.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112118 restraints weight = 4402.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.3488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6016  Z= 0.116
  Angle     :  0.533   6.736   8152  Z= 0.283
  Chirality :  0.037   0.161    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.843  13.346    816
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 21.43 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.33), residues: 752
  helix:  1.90 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.74 (0.55), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 550 
 TYR   0.028   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 318 
 TRP   0.005   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6016)
  covalent geometry    : angle       0.53316 ( 8152)
  hydrogen bonds       : bond        0.03537 (  435)
  hydrogen bonds       : angle       3.82074 ( 1305)

*********************** 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
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8979 (mt) cc_final: 0.8740 (mt)
REVERT: A  259 LYS cc_start: 0.8420 (tppt) cc_final: 0.8088 (ttmm)
REVERT: A  338 TYR cc_start: 0.8811 (m-80) cc_final: 0.8210 (m-80)
REVERT: A  418 GLN cc_start: 0.9221 (tp40) cc_final: 0.8893 (tp40)
REVERT: A  556 ASP cc_start: 0.8021 (m-30) cc_final: 0.7784 (m-30)
REVERT: B  104 LEU cc_start: 0.8974 (mt) cc_final: 0.8730 (mt)
REVERT: B  259 LYS cc_start: 0.8420 (tppt) cc_final: 0.8103 (ttmm)
REVERT: B  338 TYR cc_start: 0.8813 (m-80) cc_final: 0.8204 (m-80)
REVERT: B  418 GLN cc_start: 0.9215 (tp40) cc_final: 0.8880 (tp40)
REVERT: B  556 ASP cc_start: 0.8010 (m-30) cc_final: 0.7773 (m-30)
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.0567
  time to fit residues: 8.2785
Evaluate side-chains
  97 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 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 = 0.3815 r_free = 0.3815 target = 0.120494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.105318 restraints weight = 17502.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.108730 restraints weight = 14511.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.110498 restraints weight = 7181.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.111538 restraints weight = 5351.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.111673 restraints weight = 4280.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.3500

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= 0.124
  Angle     :  0.546   7.231   8152  Z= 0.291
  Chirality :  0.036   0.164    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.868  14.378    816
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 20.93 %
    Favored  : 77.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.33), residues: 752
  helix:  1.86 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.71 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 550 
 TYR   0.016   0.001   TYR B 302 
 PHE   0.030   0.001   PHE A 219 
 TRP   0.006   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6016)
  covalent geometry    : angle       0.54608 ( 8152)
  hydrogen bonds       : bond        0.03624 (  435)
  hydrogen bonds       : angle       3.87501 ( 1305)

*********************** 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
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8979 (mt) cc_final: 0.8736 (mt)
REVERT: A  338 TYR cc_start: 0.8829 (m-80) cc_final: 0.8256 (m-80)
REVERT: A  353 MET cc_start: 0.8587 (tpt) cc_final: 0.8103 (tpt)
REVERT: A  418 GLN cc_start: 0.9214 (tp40) cc_final: 0.8867 (tp40)
REVERT: A  556 ASP cc_start: 0.8038 (m-30) cc_final: 0.7795 (m-30)
REVERT: B  104 LEU cc_start: 0.8991 (mt) cc_final: 0.8747 (mt)
REVERT: B  338 TYR cc_start: 0.8833 (m-80) cc_final: 0.8248 (m-80)
REVERT: B  353 MET cc_start: 0.8581 (tpt) cc_final: 0.8098 (tpt)
REVERT: B  418 GLN cc_start: 0.9211 (tp40) cc_final: 0.8873 (tp40)
REVERT: B  556 ASP cc_start: 0.8026 (m-30) cc_final: 0.7787 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 107
  average time/residue: 0.0555
  time to fit residues: 8.6499
Evaluate side-chains
  103 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 96
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:    0.2980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 60 optimal weight:    0.0670
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 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 = 0.3845 r_free = 0.3845 target = 0.122264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.107234 restraints weight = 17345.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.110679 restraints weight = 15167.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.112676 restraints weight = 7443.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.113511 restraints weight = 5408.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.113633 restraints weight = 4445.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   6016  Z= 0.114
  Angle     :  0.551   7.009   8152  Z= 0.296
  Chirality :  0.037   0.167    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.833  13.902    816
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 22.26 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.33), residues: 752
  helix:  1.83 (0.22), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.59 (0.54), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 550 
 TYR   0.034   0.001   TYR A 299 
 PHE   0.035   0.001   PHE B 219 
 TRP   0.005   0.001   TRP A 120 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6016)
  covalent geometry    : angle       0.55116 ( 8152)
  hydrogen bonds       : bond        0.03487 (  435)
  hydrogen bonds       : angle       3.85749 ( 1305)

*********************** 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
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8922 (mt) cc_final: 0.8682 (mt)
REVERT: A  255 ASN cc_start: 0.8571 (m-40) cc_final: 0.8336 (m-40)
REVERT: A  338 TYR cc_start: 0.8791 (m-80) cc_final: 0.8257 (m-80)
REVERT: A  418 GLN cc_start: 0.9188 (tp40) cc_final: 0.8824 (tp40)
REVERT: A  556 ASP cc_start: 0.7973 (m-30) cc_final: 0.7765 (m-30)
REVERT: B  104 LEU cc_start: 0.8937 (mt) cc_final: 0.8654 (mp)
REVERT: B  255 ASN cc_start: 0.8565 (m-40) cc_final: 0.8330 (m-40)
REVERT: B  338 TYR cc_start: 0.8791 (m-80) cc_final: 0.8252 (m-80)
REVERT: B  418 GLN cc_start: 0.9194 (tp40) cc_final: 0.8829 (tp40)
REVERT: B  556 ASP cc_start: 0.7960 (m-30) cc_final: 0.7753 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 107
  average time/residue: 0.0535
  time to fit residues: 8.3207
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  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   99 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  395 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 69 optimal weight:    0.1980
   chunk 1 optimal weight:   10.0000
   chunk 37 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.122029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.107040 restraints weight = 17228.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.110485 restraints weight = 14413.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.112216 restraints weight = 7134.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.112268 restraints weight = 5304.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.112807 restraints weight = 5065.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6016  Z= 0.129
  Angle     :  0.620  10.438   8152  Z= 0.325
  Chirality :  0.038   0.167    942
  Planarity :  0.003   0.034   1012
  Dihedral  :  3.922  17.118    816
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 24.75 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.32), residues: 752
  helix:  1.78 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.51 (0.55), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 550 
 TYR   0.031   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 181 
 TRP   0.010   0.001   TRP B 335 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6016)
  covalent geometry    : angle       0.61968 ( 8152)
  hydrogen bonds       : bond        0.03572 (  435)
  hydrogen bonds       : angle       3.92233 ( 1305)

*********************** 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
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 94
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8923 (mt) cc_final: 0.8693 (mt)
REVERT: A  338 TYR cc_start: 0.8807 (m-80) cc_final: 0.8268 (m-80)
REVERT: A  418 GLN cc_start: 0.9188 (tp40) cc_final: 0.8806 (tp40)
REVERT: A  546 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: A  556 ASP cc_start: 0.7985 (m-30) cc_final: 0.7772 (m-30)
REVERT: B  104 LEU cc_start: 0.8921 (mt) cc_final: 0.8687 (mt)
REVERT: B  338 TYR cc_start: 0.8801 (m-80) cc_final: 0.8262 (m-80)
REVERT: B  418 GLN cc_start: 0.9209 (tp40) cc_final: 0.8836 (tp40)
REVERT: B  546 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7540 (tm-30)
REVERT: B  556 ASP cc_start: 0.7974 (m-30) cc_final: 0.7764 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 99
  average time/residue: 0.0621
  time to fit residues: 9.0701
Evaluate side-chains
  99 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   99 THR
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 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 70 optimal weight:    0.4980
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 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 = 0.3832 r_free = 0.3832 target = 0.121867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.106632 restraints weight = 17293.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.110202 restraints weight = 14730.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.112062 restraints weight = 7191.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.112909 restraints weight = 5267.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.112780 restraints weight = 4471.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6016  Z= 0.134
  Angle     :  0.663  12.076   8152  Z= 0.341
  Chirality :  0.038   0.170    942
  Planarity :  0.003   0.035   1012
  Dihedral  :  3.929  14.681    816
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 25.08 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.32), residues: 752
  helix:  1.76 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.39 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 550 
 TYR   0.032   0.001   TYR A 299 
 PHE   0.046   0.001   PHE A 219 
 TRP   0.009   0.001   TRP B 335 
 HIS   0.003   0.001   HIS B 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6016)
  covalent geometry    : angle       0.66278 ( 8152)
  hydrogen bonds       : bond        0.03639 (  435)
  hydrogen bonds       : angle       3.94167 ( 1305)

********************** 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
  101 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  104 LEU cc_start: 0.8928 (mt) cc_final: 0.8692 (mt)
REVERT: A  338 TYR cc_start: 0.8802 (m-80) cc_final: 0.8211 (m-80)
REVERT: A  418 GLN cc_start: 0.9169 (tp40) cc_final: 0.8806 (tp40)
REVERT: A  546 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7586 (tm-30)
REVERT: A  556 ASP cc_start: 0.7992 (m-30) cc_final: 0.7773 (m-30)
REVERT: B  104 LEU cc_start: 0.8936 (mt) cc_final: 0.8697 (mt)
REVERT: B  338 TYR cc_start: 0.8799 (m-80) cc_final: 0.8234 (m-80)
REVERT: B  418 GLN cc_start: 0.9184 (tp40) cc_final: 0.8812 (tp40)
REVERT: B  546 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: B  556 ASP cc_start: 0.7979 (m-30) cc_final: 0.7769 (m-30)
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.0487
  time to fit residues: 7.0239
Evaluate side-chains
  96 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 91
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue   99 THR
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 8 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0050
   chunk 43 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 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 = 0.3836 r_free = 0.3836 target = 0.122286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.107103 restraints weight = 16887.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.110638 restraints weight = 14395.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.112952 restraints weight = 7087.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.112970 restraints weight = 4995.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.113410 restraints weight = 4552.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6016  Z= 0.131
  Angle     :  0.664  10.940   8152  Z= 0.342
  Chirality :  0.038   0.167    942
  Planarity :  0.003   0.034   1012
  Dihedral  :  4.027  18.809    816
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 25.08 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.32), residues: 752
  helix:  1.70 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -2.20 (0.57), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 550 
 TYR   0.029   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 181 
 TRP   0.008   0.001   TRP A 335 
 HIS   0.003   0.001   HIS A 254 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6016)
  covalent geometry    : angle       0.66414 ( 8152)
  hydrogen bonds       : bond        0.03673 (  435)
  hydrogen bonds       : angle       4.02930 ( 1305)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 886.58 seconds
wall clock time: 16 minutes 8.02 seconds (968.02 seconds total)