Starting phenix.real_space_refine
on Tue Mar 11 15:14:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.03
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b01_15775/03_2025/8b01_15775.cif"
  }
  resolution = 3.03
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.011
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      33      5.16       5
     Na      2      4.78       5
     C    3682      2.51       5
     N     834      2.21       5
     O     925      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5478
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1257
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1257
          Classifications: {'peptide': 153}
          Link IDs: {'PTRANS': 4, 'TRANS': 148}
    Chain: "B"
      Number of atoms: 3208
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 427, 3208
          Classifications: {'peptide': 427}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 404}
    Chain: "C"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 815
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 4, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 90
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 90
          Unusual residues: {'D10': 1, 'OCT': 1, 'PTY': 1, 'TWT': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 108
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 108
          Unusual residues: {' NA': 2, 'D10': 1, 'HEX': 1, 'OCT': 5, 'PTY': 1, 'TRD': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 13
  Residues with excluded nonbonded symmetry interactions: 13
    residue:
      pdb=" C1  OCT A 201 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT A 201 " occ=0.50
    residue:
      pdb=" C1  PTY A 202 " occ=0.50
      ... (48 atoms not shown)
      pdb=" P1  PTY A 202 " occ=0.50
    residue:
      pdb=" C1  TWT A 203 " occ=0.50
      ... (20 atoms not shown)
      pdb=" C9  TWT A 203 " occ=0.50
    residue:
      pdb=" C1  D10 A 204 " occ=0.50
      ... (8 atoms not shown)
      pdb=" C9  D10 A 204 " occ=0.50
    residue:
      pdb=" C1  OCT B 503 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT B 503 " occ=0.50
    residue:
      pdb=" C1  OCT B 504 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT B 504 " occ=0.50
    residue:
      pdb=" C1  OCT B 505 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT B 505 " occ=0.50
    residue:
      pdb=" C1  OCT B 506 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT B 506 " occ=0.50
    residue:
      pdb=" C1  OCT B 507 " occ=0.50
      ... (6 atoms not shown)
      pdb=" C8  OCT B 507 " occ=0.50
    residue:
      pdb=" C1  TRD B 508 " occ=0.50
      ... (11 atoms not shown)
      pdb=" C9  TRD B 508 " occ=0.50
    residue:
      pdb=" C1  D10 B 509 " occ=0.50
      ... (8 atoms not shown)
      pdb=" C9  D10 B 509 " occ=0.50
    residue:
      pdb=" C1  PTY B 510 " occ=0.50
      ... (35 atoms not shown)
      pdb=" P1  PTY B 510 " occ=0.50
    residue:
      pdb=" C1  HEX B 511 " occ=0.50
      ... (4 atoms not shown)
      pdb=" C6  HEX B 511 " occ=0.50
  Time building chain proxies: 4.14, per 1000 atoms: 0.76
  Number of scatterers: 5478
  At special positions: 0
  Unit cell: (91.258, 77.082, 92.144, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      33     16.00
     P       2     15.00
     Na      2     11.00
     O     925      8.00
     N     834      7.00
     C    3682      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.06
  Conformation dependent library (CDL) restraints added in 845.9 milliseconds
  

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1248

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 3 sheets defined
      74.0% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
      removed outlier: 3.527A  pdb=" N   ILE A   6 " --> pdb=" O   PHE A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 35
      Proline residue:  A  16  - end of helix
    Processing helix  chain 'A' and resid 41 through 64
      removed outlier: 3.579A  pdb=" N   LEU A  45 " --> pdb=" O   TRP A  41 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLY A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ALA A  59 " --> pdb=" O   ILE A  55 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ILE A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.723A  pdb=" N   LYS A  76 " --> pdb=" O   PHE A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 111
      removed outlier: 3.864A  pdb=" N   LEU A  85 " --> pdb=" O   PHE A  81 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   ALA A  88 " --> pdb=" O   SER A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 128
    Processing helix  chain 'A' and resid 128 through 152
      removed outlier: 3.655A  pdb=" N   PHE A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR A 146 " --> pdb=" O   CYS A 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.675A  pdb=" N   GLY B  15 " --> pdb=" O   LEU B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 33
    Processing helix  chain 'B' and resid 35 through 39
      removed outlier: 3.760A  pdb=" N   ILE B  38 " --> pdb=" O   SER B  35 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN B  39 " --> pdb=" O   THR B  36 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 35 through 39'
    Processing helix  chain 'B' and resid 40 through 50
      removed outlier: 4.075A  pdb=" N   LEU B  49 " --> pdb=" O   MET B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 55 through 70
      removed outlier: 4.046A  pdb=" N   PHE B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 85
      removed outlier: 4.205A  pdb=" N   ARG B  75 " --> pdb=" O   GLY B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 104
    Processing helix  chain 'B' and resid 108 through 127
      removed outlier: 3.594A  pdb=" N   ASP B 112 " --> pdb=" O   SER B 108 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   GLN B 118 " --> pdb=" O   GLY B 114 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU B 119 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA B 127 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 142
      removed outlier: 3.855A  pdb=" N   CYS B 142 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 148
      removed outlier: 4.023A  pdb=" N   LEU B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 162
    Processing helix  chain 'B' and resid 164 through 172
    Processing helix  chain 'B' and resid 172 through 195
      removed outlier: 4.094A  pdb=" N   GLY B 176 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 213
    Processing helix  chain 'B' and resid 215 through 217
      No H-bonds generated for 'chain 'B' and resid 215 through 217'
    Processing helix  chain 'B' and resid 218 through 230
      removed outlier: 4.251A  pdb=" N   PHE B 222 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 234 through 252
    Processing helix  chain 'B' and resid 258 through 292
      removed outlier: 3.740A  pdb=" N   MET B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 307
      removed outlier: 3.944A  pdb=" N   GLN B 298 " --> pdb=" O   GLN B 294 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ILE B 306 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   SER B 307 " --> pdb=" O   PHE B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 325
    Processing helix  chain 'B' and resid 329 through 337
    Processing helix  chain 'B' and resid 337 through 349
      Proline residue:  B 343  - end of helix
      removed outlier: 3.719A  pdb=" N   VAL B 348 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 367
    Processing helix  chain 'B' and resid 373 through 384
    Processing helix  chain 'B' and resid 386 through 395
    Processing helix  chain 'B' and resid 398 through 411
    Processing helix  chain 'B' and resid 412 through 423
      removed outlier: 4.971A  pdb=" N   LEU B 418 " --> pdb=" O   ILE B 414 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116
      removed outlier: 3.733A  pdb=" N   ILE A 121 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 17 through 22
      removed outlier: 3.620A  pdb=" N   LEU C  20 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL C  78 " --> pdb=" O   CYS C  22 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 57 through 59
      removed outlier: 5.350A  pdb=" N   LEU C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ARG C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA C  49 " --> pdb=" O   TRP C  36 " (cutoff:3.500A)

    357 hydrogen bonds defined for protein.
    1056 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 847
        1.32 -     1.45: 1431
        1.45 -     1.57: 3249
        1.57 -     1.69: 4
        1.69 -     1.81: 57
  Bond restraints: 5588
  Sorted by residual:
  bond pdb=" C   GLY B 231 "
       pdb=" N   LYS B 232 "
    ideal  model  delta    sigma   weight residual
    1.334  1.284  0.050 1.46e-02 4.69e+03 1.17e+01
  bond pdb=" N   VAL B 283 "
       pdb=" CA  VAL B 283 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.19e-02 7.06e+03 8.33e+00
  bond pdb=" N   TYR C 107 "
       pdb=" CA  TYR C 107 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.31e-02 5.83e+03 7.71e+00
  bond pdb=" N   SER B 106 "
       pdb=" CA  SER B 106 "
    ideal  model  delta    sigma   weight residual
    1.454  1.486 -0.032 1.17e-02 7.31e+03 7.48e+00
  bond pdb=" CA  TYR C 105 "
       pdb=" C   TYR C 105 "
    ideal  model  delta    sigma   weight residual
    1.524  1.557 -0.033 1.32e-02 5.74e+03 6.25e+00
  ... (remaining 5583 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 7288
        1.47 -     2.94: 195
        2.94 -     4.42: 35
        4.42 -     5.89: 13
        5.89 -     7.36: 3
  Bond angle restraints: 7534
  Sorted by residual:
  angle pdb=" N   PRO C 104 "
        pdb=" CA  PRO C 104 "
        pdb=" C   PRO C 104 "
      ideal   model   delta    sigma   weight residual
     113.40  106.04    7.36 1.34e+00 5.57e-01 3.02e+01
  angle pdb=" N   PHE B 102 "
        pdb=" CA  PHE B 102 "
        pdb=" C   PHE B 102 "
      ideal   model   delta    sigma   weight residual
     112.54  107.68    4.86 1.22e+00 6.72e-01 1.59e+01
  angle pdb=" N   LEU B 321 "
        pdb=" CA  LEU B 321 "
        pdb=" C   LEU B 321 "
      ideal   model   delta    sigma   weight residual
     111.14  106.89    4.25 1.08e+00 8.57e-01 1.55e+01
  angle pdb=" N   TYR A 128 "
        pdb=" CA  TYR A 128 "
        pdb=" C   TYR A 128 "
      ideal   model   delta    sigma   weight residual
     113.15  108.69    4.46 1.19e+00 7.06e-01 1.41e+01
  angle pdb=" CA  TYR C 101 "
        pdb=" C   TYR C 101 "
        pdb=" O   TYR C 101 "
      ideal   model   delta    sigma   weight residual
     121.49  117.51    3.98 1.16e+00 7.43e-01 1.18e+01
  ... (remaining 7529 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.16: 2984
       17.16 -    34.32: 246
       34.32 -    51.48: 57
       51.48 -    68.64: 12
       68.64 -    85.80: 3
  Dihedral angle restraints: 3302
    sinusoidal: 1346
      harmonic: 1956
  Sorted by residual:
  dihedral pdb=" CA  PHE B 233 "
           pdb=" C   PHE B 233 "
           pdb=" N   THR B 234 "
           pdb=" CA  THR B 234 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ASP B 131 "
           pdb=" CB  ASP B 131 "
           pdb=" CG  ASP B 131 "
           pdb=" OD1 ASP B 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.28   59.28     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CG  ARG C  71 "
           pdb=" CD  ARG C  71 "
           pdb=" NE  ARG C  71 "
           pdb=" CZ  ARG C  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.72  -44.72     2      1.50e+01 4.44e-03 1.06e+01
  ... (remaining 3299 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 699
       0.051 -    0.102: 151
       0.102 -    0.153: 27
       0.153 -    0.203: 3
       0.203 -    0.254: 2
  Chirality restraints: 882
  Sorted by residual:
  chirality pdb=" CA  LEU B 321 "
            pdb=" N   LEU B 321 "
            pdb=" C   LEU B 321 "
            pdb=" CB  LEU B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  PRO C 104 "
            pdb=" N   PRO C 104 "
            pdb=" C   PRO C 104 "
            pdb=" CB  PRO C 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.93   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  LEU B 322 "
            pdb=" N   LEU B 322 "
            pdb=" C   LEU B 322 "
            pdb=" CB  LEU B 322 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.23e-01
  ... (remaining 879 not shown)

  Planarity restraints: 901
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 105 "   -0.012 2.00e-02 2.50e+03   2.36e-02 5.57e+00
        pdb=" C   TYR C 105 "    0.041 2.00e-02 2.50e+03
        pdb=" O   TYR C 105 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   TYR C 106 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 127 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   THR A 127 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR A 127 "    0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A 128 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 234 "    0.031 5.00e-02 4.00e+02   4.66e-02 3.48e+00
        pdb=" N   PRO B 235 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 235 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 235 "    0.026 5.00e-02 4.00e+02
  ... (remaining 898 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 821
        2.75 -     3.29: 5229
        3.29 -     3.83: 8542
        3.83 -     4.36: 9479
        4.36 -     4.90: 17735
  Nonbonded interactions: 41806
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 351 "
            pdb=" OH  TYR B 425 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OH  TYR C  37 "
            pdb=" O   TYR C  98 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   GLY B 145 "
            pdb="NA    NA B 501 "
     model   vdw
     2.282 2.470
  nonbonded pdb=" NH1 ARG A  32 "
            pdb=" OE2 GLU B 237 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" NE2 GLN C  39 "
            pdb=" O   LYS C  43 "
     model   vdw
     2.311 3.120
  ... (remaining 41801 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.530
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.720
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
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   0.050   5588  Z= 0.262
  Angle     :  0.598   7.359   7534  Z= 0.362
  Chirality :  0.043   0.254    882
  Planarity :  0.005   0.047    901
  Dihedral  : 13.526  85.796   2051
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  0.53 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.33), residues: 678
  helix:  2.35 (0.25), residues: 457
  sheet: -0.48 (0.96), residues: 33
  loop : -0.54 (0.43), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  27 
 HIS   0.003   0.001   HIS B  86 
 PHE   0.011   0.001   PHE B  59 
 TYR   0.022   0.001   TYR A 128 
 ARG   0.002   0.000   ARG B  75 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 0.638 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6900 (mmm160)
REVERT: A    4 LYS cc_start: 0.8466 (tppp) cc_final: 0.7601 (ptpt)
REVERT: B  118 GLN cc_start: 0.7449 (tp40) cc_final: 0.7135 (tp-100)
REVERT: B  122 LYS cc_start: 0.8294 (ttpt) cc_final: 0.7897 (tptp)
REVERT: B  126 ASP cc_start: 0.9056 (m-30) cc_final: 0.8363 (m-30)
REVERT: B  372 MET cc_start: 0.8171 (tmm) cc_final: 0.7735 (tmm)
REVERT: B  392 ARG cc_start: 0.8307 (ttm170) cc_final: 0.7949 (ttp80)
REVERT: C   34 MET cc_start: 0.8192 (tpp) cc_final: 0.7867 (tpp)
REVERT: C   72 ASP cc_start: 0.8378 (t70) cc_final: 0.8036 (t0)
REVERT: C   85 LEU cc_start: 0.8107 (mt) cc_final: 0.7861 (mt)
REVERT: C  108 TRP cc_start: 0.7247 (m-10) cc_final: 0.6801 (m-10)
  outliers start: 3
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2326
  time to fit residues: 31.7185
Evaluate side-chains
  85 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 52 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  67 HIS
B 354 HIS
B 384 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.088815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.074163 restraints weight = 10514.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.61
r_work: 0.2890 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5588  Z= 0.189
  Angle     :  0.538   7.916   7534  Z= 0.275
  Chirality :  0.039   0.147    882
  Planarity :  0.005   0.049    901
  Dihedral  :  8.992  87.212    879
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  5.79 %
    Favored  : 93.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.33), residues: 678
  helix:  2.55 (0.24), residues: 458
  sheet: -0.79 (0.93), residues: 34
  loop : -0.32 (0.43), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B   8 
 HIS   0.002   0.001   HIS B 354 
 PHE   0.024   0.001   PHE A   2 
 TYR   0.011   0.001   TYR B 425 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8435 (tppp) cc_final: 0.7788 (pttt)
REVERT: B  105 MET cc_start: 0.7771 (mtt) cc_final: 0.7505 (mtt)
REVERT: B  118 GLN cc_start: 0.7727 (tp40) cc_final: 0.7433 (tp-100)
REVERT: B  126 ASP cc_start: 0.8865 (m-30) cc_final: 0.8409 (m-30)
REVERT: B  392 ARG cc_start: 0.8552 (ttm170) cc_final: 0.8217 (ttp80)
REVERT: C   34 MET cc_start: 0.8293 (tpp) cc_final: 0.7917 (tpp)
REVERT: C   72 ASP cc_start: 0.8433 (t70) cc_final: 0.8016 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 90
  average time/residue: 0.2047
  time to fit residues: 23.4683
Evaluate side-chains
  85 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 66 optimal weight:    8.9990
   chunk 33 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.086461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.072236 restraints weight = 10653.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.65
r_work: 0.2857 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2868
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2868 r_free = 0.2868    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2864 r_free = 0.2864    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2864
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5588  Z= 0.204
  Angle     :  0.513   7.624   7534  Z= 0.262
  Chirality :  0.038   0.143    882
  Planarity :  0.005   0.048    901
  Dihedral  :  8.931  88.070    879
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.25 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.33), residues: 678
  helix:  2.58 (0.24), residues: 459
  sheet: -1.10 (0.89), residues: 34
  loop : -0.42 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 108 
 HIS   0.003   0.001   HIS B  86 
 PHE   0.017   0.001   PHE A   2 
 TYR   0.011   0.001   TYR C  94 
 ARG   0.004   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 84
  time to evaluate  : 0.662 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8364 (tppp) cc_final: 0.7750 (pttt)
REVERT: B  105 MET cc_start: 0.7948 (mtt) cc_final: 0.7691 (mtt)
REVERT: B  118 GLN cc_start: 0.7729 (tp40) cc_final: 0.7440 (tp-100)
REVERT: B  126 ASP cc_start: 0.8805 (m-30) cc_final: 0.8389 (m-30)
REVERT: B  392 ARG cc_start: 0.8533 (ttm170) cc_final: 0.8191 (ttp80)
REVERT: C   72 ASP cc_start: 0.8437 (t70) cc_final: 0.8024 (t0)
REVERT: C   88 GLU cc_start: 0.8255 (mp0) cc_final: 0.7793 (mp0)
  outliers start: 4
  outliers final: 4
  residues processed: 86
  average time/residue: 0.2175
  time to fit residues: 23.6779
Evaluate side-chains
  86 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 318 ASN
B 384 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.087255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.073322 restraints weight = 11034.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.50
r_work: 0.2918 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2928 r_free = 0.2928    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2928
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5588  Z= 0.177
  Angle     :  0.492   7.265   7534  Z= 0.251
  Chirality :  0.037   0.144    882
  Planarity :  0.004   0.049    901
  Dihedral  :  8.792  88.824    879
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.12 %
    Favored  : 88.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.33), residues: 678
  helix:  2.74 (0.24), residues: 455
  sheet: -1.22 (0.89), residues: 34
  loop : -0.32 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  27 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.013   0.001   PHE A   2 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.004   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.553 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8431 (tppp) cc_final: 0.7815 (pttt)
REVERT: B  105 MET cc_start: 0.8131 (mtt) cc_final: 0.7905 (mtt)
REVERT: B  118 GLN cc_start: 0.7761 (tp40) cc_final: 0.7506 (tp-100)
REVERT: B  126 ASP cc_start: 0.8765 (m-30) cc_final: 0.8397 (m-30)
REVERT: B  392 ARG cc_start: 0.8522 (ttm170) cc_final: 0.8251 (ttp80)
REVERT: C   72 ASP cc_start: 0.8535 (t70) cc_final: 0.8192 (t0)
REVERT: C  103 ASP cc_start: 0.7765 (OUTLIER) cc_final: 0.7269 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 91
  average time/residue: 0.1974
  time to fit residues: 22.9642
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.087207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.073294 restraints weight = 10894.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.50
r_work: 0.2921 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5588  Z= 0.169
  Angle     :  0.482   7.188   7534  Z= 0.245
  Chirality :  0.037   0.138    882
  Planarity :  0.004   0.048    901
  Dihedral  :  8.672  89.574    879
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 10.53 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.33), residues: 678
  helix:  2.80 (0.24), residues: 455
  sheet: -1.29 (0.91), residues: 34
  loop : -0.33 (0.43), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  27 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.011   0.001   PHE A   2 
 TYR   0.009   0.001   TYR C  94 
 ARG   0.004   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.732 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8440 (tppp) cc_final: 0.7802 (pttt)
REVERT: B  105 MET cc_start: 0.8153 (mtt) cc_final: 0.7950 (mtt)
REVERT: B  118 GLN cc_start: 0.7723 (tp40) cc_final: 0.7474 (tp-100)
REVERT: B  126 ASP cc_start: 0.8767 (m-30) cc_final: 0.8407 (m-30)
REVERT: B  392 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8253 (ttp80)
REVERT: C   72 ASP cc_start: 0.8553 (t70) cc_final: 0.8225 (t0)
REVERT: C  100 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6914 (pt)
REVERT: C  103 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7420 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 89
  average time/residue: 0.2033
  time to fit residues: 23.7763
Evaluate side-chains
  90 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.1342

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN
C  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.084869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.070625 restraints weight = 10742.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 2.58
r_work: 0.2850 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2861
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2861 r_free = 0.2861    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2861
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5588  Z= 0.240
  Angle     :  0.516   7.718   7534  Z= 0.262
  Chirality :  0.038   0.146    882
  Planarity :  0.005   0.048    901
  Dihedral  :  8.783  89.206    879
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 10.53 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.50 (0.33), residues: 678
  helix:  2.70 (0.24), residues: 456
  sheet: -1.31 (0.91), residues: 34
  loop : -0.46 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  33 
 HIS   0.003   0.001   HIS B  86 
 PHE   0.011   0.001   PHE A   2 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.622 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8408 (tppp) cc_final: 0.7877 (pttt)
REVERT: B  118 GLN cc_start: 0.7763 (tp40) cc_final: 0.7490 (tp-100)
REVERT: B  126 ASP cc_start: 0.8745 (m-30) cc_final: 0.8372 (m-30)
REVERT: B  392 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8221 (ttp80)
REVERT: C   72 ASP cc_start: 0.8546 (t70) cc_final: 0.7923 (t0)
REVERT: C   75 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8467 (mtmm)
REVERT: C  100 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6932 (pt)
REVERT: C  103 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7334 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1928
  time to fit residues: 21.6907
Evaluate side-chains
  88 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 76
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.086237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.071918 restraints weight = 10826.340|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.61
r_work: 0.2875 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5588  Z= 0.175
  Angle     :  0.487   7.253   7534  Z= 0.249
  Chirality :  0.037   0.143    882
  Planarity :  0.004   0.048    901
  Dihedral  :  8.677  89.884    879
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 1.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.23 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.56 (0.33), residues: 678
  helix:  2.77 (0.24), residues: 456
  sheet: -1.40 (0.92), residues: 34
  loop : -0.46 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  27 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.010   0.001   PHE A   2 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.594 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8397 (tppp) cc_final: 0.7857 (pttt)
REVERT: B  118 GLN cc_start: 0.7701 (tp40) cc_final: 0.7441 (tp-100)
REVERT: B  126 ASP cc_start: 0.8701 (m-30) cc_final: 0.8314 (m-30)
REVERT: B  384 ASN cc_start: 0.9120 (OUTLIER) cc_final: 0.8879 (t0)
REVERT: B  392 ARG cc_start: 0.8551 (ttm170) cc_final: 0.8209 (ttp80)
REVERT: C   46 GLU cc_start: 0.8180 (tt0) cc_final: 0.7889 (tt0)
REVERT: C   72 ASP cc_start: 0.8536 (t70) cc_final: 0.8194 (t0)
REVERT: C  103 ASP cc_start: 0.7961 (OUTLIER) cc_final: 0.7400 (t0)
  outliers start: 12
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1893
  time to fit residues: 21.0506
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  384 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0870
   chunk 61 optimal weight:    0.0980
   chunk 55 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 45 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.087336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.073025 restraints weight = 10798.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.58
r_work: 0.2893 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2901 r_free = 0.2901    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5588  Z= 0.143
  Angle     :  0.476   7.022   7534  Z= 0.244
  Chirality :  0.037   0.144    882
  Planarity :  0.004   0.047    901
  Dihedral  :  8.512  89.433    879
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.40 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.33), residues: 678
  helix:  2.82 (0.24), residues: 456
  sheet: -1.46 (0.92), residues: 34
  loop : -0.42 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 108 
 HIS   0.002   0.000   HIS B 388 
 PHE   0.009   0.001   PHE A   2 
 TYR   0.009   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.607 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8405 (tppp) cc_final: 0.7854 (pttt)
REVERT: B  118 GLN cc_start: 0.7682 (tp40) cc_final: 0.7436 (tp-100)
REVERT: B  126 ASP cc_start: 0.8688 (m-30) cc_final: 0.8301 (m-30)
REVERT: B  392 ARG cc_start: 0.8547 (ttm170) cc_final: 0.8261 (ttp80)
REVERT: C   46 GLU cc_start: 0.8215 (tt0) cc_final: 0.7914 (tt0)
REVERT: C   72 ASP cc_start: 0.8558 (t70) cc_final: 0.8223 (t0)
REVERT: C  100 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6849 (pt)
REVERT: C  103 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7393 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.1976
  time to fit residues: 22.8562
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.086758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.072476 restraints weight = 10819.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.57
r_work: 0.2881 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2888
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2888 r_free = 0.2888    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2888
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5588  Z= 0.179
  Angle     :  0.494   7.182   7534  Z= 0.251
  Chirality :  0.037   0.143    882
  Planarity :  0.004   0.047    901
  Dihedral  :  8.453  89.418    879
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.58 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.33), residues: 678
  helix:  2.84 (0.24), residues: 456
  sheet: -1.41 (0.91), residues: 34
  loop : -0.42 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 108 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.009   0.001   PHE A   2 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.565 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8410 (tppp) cc_final: 0.7864 (pttt)
REVERT: B  118 GLN cc_start: 0.7722 (tp40) cc_final: 0.7473 (tp-100)
REVERT: B  126 ASP cc_start: 0.8698 (m-30) cc_final: 0.8325 (m-30)
REVERT: B  384 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8870 (t0)
REVERT: B  392 ARG cc_start: 0.8541 (ttm170) cc_final: 0.8199 (ttp80)
REVERT: C   46 GLU cc_start: 0.8226 (tt0) cc_final: 0.7921 (tt0)
REVERT: C   72 ASP cc_start: 0.8576 (t70) cc_final: 0.8245 (t0)
REVERT: C  100 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6834 (pt)
REVERT: C  103 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7380 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1952
  time to fit residues: 21.6978
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  384 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.086125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.071906 restraints weight = 10784.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 2.59
r_work: 0.2881 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2891
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2891 r_free = 0.2891    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2891
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5588  Z= 0.181
  Angle     :  0.496   7.185   7534  Z= 0.252
  Chirality :  0.037   0.143    882
  Planarity :  0.004   0.047    901
  Dihedral  :  8.424  89.253    879
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 2.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.58 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.33), residues: 678
  helix:  2.84 (0.24), residues: 456
  sheet: -1.39 (0.91), residues: 34
  loop : -0.41 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.010   0.001   PHE A   2 
 TYR   0.010   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 

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

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

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1356 Ramachandran restraints generated.
    678 Oldfield, 0 Emsley, 678 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A    4 LYS cc_start: 0.8416 (tppp) cc_final: 0.7868 (pttt)
REVERT: B  118 GLN cc_start: 0.7728 (tp40) cc_final: 0.7476 (tp-100)
REVERT: B  126 ASP cc_start: 0.8699 (m-30) cc_final: 0.8319 (m-30)
REVERT: B  392 ARG cc_start: 0.8535 (ttm170) cc_final: 0.8193 (ttp80)
REVERT: C   46 GLU cc_start: 0.8228 (tt0) cc_final: 0.7914 (tt0)
REVERT: C   72 ASP cc_start: 0.8578 (t70) cc_final: 0.7995 (t0)
REVERT: C   75 LYS cc_start: 0.9222 (mtmm) cc_final: 0.8542 (mtmm)
REVERT: C  100 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6843 (pt)
REVERT: C  103 ASP cc_start: 0.7894 (OUTLIER) cc_final: 0.7376 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1989
  time to fit residues: 22.1141
Evaluate side-chains
  91 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 SER
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain B residue  258 THR
Chi-restraints excluded: chain B residue  358 MET
Chi-restraints excluded: chain B residue  367 ILE
Chi-restraints excluded: chain B residue  384 ASN
Chi-restraints excluded: chain C residue   56 SER
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   86 LYS
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  103 ASP
Chi-restraints excluded: chain C residue  112 THR
Chi-restraints excluded: chain C residue  114 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 67
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0000
   chunk 16 optimal weight:    0.9990
   chunk 60 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
B 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.086299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.072032 restraints weight = 10846.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3013 rms_B_bonded: 2.60
r_work: 0.2884 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2893 r_free = 0.2893    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.2893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5588  Z= 0.171
  Angle     :  0.492   7.130   7534  Z= 0.251
  Chirality :  0.037   0.143    882
  Planarity :  0.004   0.047    901
  Dihedral  :  8.374  88.955    879
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 11.58 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.33), residues: 678
  helix:  2.85 (0.24), residues: 456
  sheet: -1.38 (0.91), residues: 34
  loop : -0.44 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 108 
 HIS   0.002   0.001   HIS B  86 
 PHE   0.009   0.001   PHE A   2 
 TYR   0.009   0.001   TYR C  94 
 ARG   0.003   0.000   ARG A  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2663.82 seconds
wall clock time: 46 minutes 20.55 seconds (2780.55 seconds total)