Starting phenix.real_space_refine
on Tue Mar  3 18:33:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7k0j_22599/03_2026/7k0j_22599.map"
  }
  resolution = 3.1
  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=  -0.002 sd=   0.073
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      44      5.16       5
     C    4920      2.51       5
     N    1305      2.21       5
     O    1413      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7683
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 423, 3287
          Classifications: {'peptide': 423}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 21, 'TRANS': 401}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 3883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3883
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 17, 'TRANS': 474}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 476
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 476
          Classifications: {'peptide': 62}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 2, 'TRANS': 59}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 79
          Unresolved non-hydrogen dihedrals: 56
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 22
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 82
          Unresolved non-hydrogen angles: 100
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 2, 'POV:plan-3': 2}
          Unresolved non-hydrogen planarities: 24
  Time building chain proxies: 1.86, per 1000 atoms: 0.24
  Number of scatterers: 7683
  At special positions: 0
  Unit cell: (88.044, 81.0405, 128.064, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P       1     15.00
     O    1413      8.00
     N    1305      7.00
     C    4920      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 309.3 milliseconds
  

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1804

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      51.1% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 77 through 81
    Processing helix  chain 'A' and resid 114 through 129
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.673A  pdb=" N   LEU A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 179
      removed outlier: 4.536A  pdb=" N   ILE A 171 " --> pdb=" O   GLY A 167 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 192 through 202
    Processing helix  chain 'A' and resid 213 through 231
    Processing helix  chain 'A' and resid 231 through 236
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 321 through 326
    Processing helix  chain 'A' and resid 327 through 332
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 342 through 359
      removed outlier: 3.694A  pdb=" N   ASN A 359 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 377
      removed outlier: 4.070A  pdb=" N   ALA A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 422
      removed outlier: 3.615A  pdb=" N   ARG A 422 " --> pdb=" O   GLN A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 472
    Processing helix  chain 'B' and resid 67 through 94
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 3.588A  pdb=" N   LYS B 109 " --> pdb=" O   GLU B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 126
      removed outlier: 3.784A  pdb=" N   ASN B 120 " --> pdb=" O   GLN B 116 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   TYR B 122 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 5.632A  pdb=" N   THR B 123 " --> pdb=" O   GLU B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 134
      removed outlier: 5.684A  pdb=" N   ASP B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 200
    Processing helix  chain 'B' and resid 213 through 228
      removed outlier: 3.621A  pdb=" N   GLU B 217 " --> pdb=" O   LEU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 250
      Proline residue:  B 247  - end of helix
      removed outlier: 3.559A  pdb=" N   VAL B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 273
    Processing helix  chain 'B' and resid 284 through 298
    Processing helix  chain 'B' and resid 326 through 337
    Processing helix  chain 'B' and resid 358 through 363
    Processing helix  chain 'B' and resid 391 through 402
    Processing helix  chain 'B' and resid 402 through 408
    Processing helix  chain 'B' and resid 412 through 427
    Processing helix  chain 'B' and resid 433 through 455
      removed outlier: 3.576A  pdb=" N   GLU B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL B 439 " --> pdb=" O   GLY B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 489
      removed outlier: 3.901A  pdb=" N   GLY B 480 " --> pdb=" O   PRO B 476 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY B 483 " --> pdb=" O   ILE B 479 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ARG B 489 " --> pdb=" O   GLU B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 536
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 30 through 55
    Processing helix  chain 'C' and resid 58 through 69
    Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.883A  pdb=" N   ALA A 425 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164
      removed outlier: 7.052A  pdb=" N   ILE A 271 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   SER A 304 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   LEU A 273 " --> pdb=" O   SER A 304 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ARG A 240 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   PHE A 272 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 6.165A  pdb=" N   ILE A 242 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 7.612A  pdb=" N   GLU A 274 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL A 244 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 386
      removed outlier: 4.069A  pdb=" N   THR A 427 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 153
      removed outlier: 6.734A  pdb=" N   VAL B 146 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   ILE B 167 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ILE B 148 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 7.674A  pdb=" N   ASN B 165 " --> pdb=" O   ILE B 148 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   GLU B 150 " --> pdb=" O   THR B 163 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   GLY B 492 " --> pdb=" O   GLY B 169 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   ILE B 171 " --> pdb=" O   GLY B 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 231 through 235
      removed outlier: 6.644A  pdb=" N   ILE B 310 " --> pdb=" O   TYR B 340 " (cutoff:3.500A)
      removed outlier: 7.589A  pdb=" N   TYR B 342 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   ILE B 312 " --> pdb=" O   TYR B 342 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ASP B 344 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL B 314 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ASP B 259 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   GLU B 315 " --> pdb=" O   ASP B 259 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 468 through 472
      removed outlier: 3.860A  pdb=" N   VAL B 494 " --> pdb=" O   ARG B 509 " (cutoff:3.500A)

    391 hydrogen bonds defined for protein.
    1122 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: 1.17

  Time building geometry restraints manager: 1.05 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: 2500
        1.34 -     1.46: 1123
        1.46 -     1.57: 4144
        1.57 -     1.69: 1
        1.69 -     1.81: 71
  Bond restraints: 7839
  Sorted by residual:
  bond pdb=" N   PHE B 121 "
       pdb=" CA  PHE B 121 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.16e-02 7.43e+03 7.12e+00
  bond pdb=" N   ASN B 120 "
       pdb=" CA  ASN B 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.32e-02 5.74e+03 6.21e+00
  bond pdb=" N   GLU B 119 "
       pdb=" CA  GLU B 119 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.029 1.21e-02 6.83e+03 5.91e+00
  bond pdb=" N   PHE B 118 "
       pdb=" CA  PHE B 118 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.25e-02 6.40e+03 5.80e+00
  bond pdb=" C   ARG A 287 "
       pdb=" N   GLY A 288 "
    ideal  model  delta    sigma   weight residual
    1.334  1.318  0.016 1.12e-02 7.97e+03 1.95e+00
  ... (remaining 7834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 10377
        2.06 -     4.11: 190
        4.11 -     6.17: 20
        6.17 -     8.23: 2
        8.23 -    10.28: 2
  Bond angle restraints: 10591
  Sorted by residual:
  angle pdb=" C   GLY B 497 "
        pdb=" N   PHE B 498 "
        pdb=" CA  PHE B 498 "
      ideal   model   delta    sigma   weight residual
     120.09  125.22   -5.13 1.25e+00 6.40e-01 1.68e+01
  angle pdb=" C   VAL A 130 "
        pdb=" N   GLY A 131 "
        pdb=" CA  GLY A 131 "
      ideal   model   delta    sigma   weight residual
     122.18  119.85    2.33 6.90e-01 2.10e+00 1.14e+01
  angle pdb=" C   LEU B 365 "
        pdb=" N   ASP B 366 "
        pdb=" CA  ASP B 366 "
      ideal   model   delta    sigma   weight residual
     121.59  131.87  -10.28 3.54e+00 7.98e-02 8.44e+00
  angle pdb=" CA  PHE B 121 "
        pdb=" C   PHE B 121 "
        pdb=" O   PHE B 121 "
      ideal   model   delta    sigma   weight residual
     121.07  117.93    3.14 1.10e+00 8.26e-01 8.17e+00
  angle pdb=" C   ILE B 426 "
        pdb=" N   MET B 427 "
        pdb=" CA  MET B 427 "
      ideal   model   delta    sigma   weight residual
     122.65  118.00    4.65 1.66e+00 3.63e-01 7.83e+00
  ... (remaining 10586 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4320
       17.92 -    35.85: 329
       35.85 -    53.77: 56
       53.77 -    71.69: 5
       71.69 -    89.62: 7
  Dihedral angle restraints: 4717
    sinusoidal: 1894
      harmonic: 2823
  Sorted by residual:
  dihedral pdb=" CA  TYR B 461 "
           pdb=" C   TYR B 461 "
           pdb=" N   GLY B 462 "
           pdb=" CA  GLY B 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.41   16.59     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  MET C  28 "
           pdb=" C   MET C  28 "
           pdb=" N   LEU C  29 "
           pdb=" CA  LEU C  29 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.55  -16.45     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CB  GLU A 451 "
           pdb=" CG  GLU A 451 "
           pdb=" CD  GLU A 451 "
           pdb=" OE1 GLU A 451 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.62  -89.62     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 4714 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 705
       0.036 -    0.071: 320
       0.071 -    0.107: 108
       0.107 -    0.143: 35
       0.143 -    0.178: 1
  Chirality restraints: 1169
  Sorted by residual:
  chirality pdb=" CB  ILE B 388 "
            pdb=" CA  ILE B 388 "
            pdb=" CG1 ILE B 388 "
            pdb=" CG2 ILE B 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.94e-01
  chirality pdb=" CA  LEU A 257 "
            pdb=" N   LEU A 257 "
            pdb=" C   LEU A 257 "
            pdb=" CB  LEU A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  ILE A 242 "
            pdb=" N   ILE A 242 "
            pdb=" C   ILE A 242 "
            pdb=" CB  ILE A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1166 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 166 "    0.016 2.00e-02 2.50e+03   1.20e-02 2.88e+00
        pdb=" CG  TYR A 166 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 166 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 166 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 166 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 166 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 166 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 166 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 469 "   -0.027 5.00e-02 4.00e+02   4.14e-02 2.75e+00
        pdb=" N   PRO B 470 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 498 "    0.028 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO B 499 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 499 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 499 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1091
        2.75 -     3.29: 7066
        3.29 -     3.82: 12146
        3.82 -     4.36: 14558
        4.36 -     4.90: 26836
  Nonbonded interactions: 61697
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 228 "
            pdb=" NH2 ARG A 240 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" OE2 GLU A 274 "
            pdb=" OG  SER A 276 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   GLU A  67 "
            pdb=" OH  TYR B 340 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG1 THR B 378 "
            pdb=" O3P PLP B 601 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" NH2 ARG A 270 "
            pdb=" OE2 GLU B 104 "
     model   vdw
     2.314 3.120
  ... (remaining 61692 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=1.00 max=1.00 mean=1.00
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:             4.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.880
  Find NCS groups from input model:        0.040
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
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      :  0.006   0.043   7840  Z= 0.267
  Angle     :  0.712  10.284  10591  Z= 0.407
  Chirality :  0.046   0.178   1169
  Planarity :  0.004   0.041   1360
  Dihedral  : 13.138  89.617   2913
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.26), residues: 971
  helix:  1.30 (0.24), residues: 444
  sheet: -0.62 (0.50), residues: 113
  loop : -0.92 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 233 
 TYR   0.029   0.002   TYR A 166 
 PHE   0.019   0.002   PHE A 168 
 TRP   0.013   0.001   TRP C  32 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 7839)
  covalent geometry    : angle       0.71226 (10591)
  hydrogen bonds       : bond        0.14908 (  391)
  hydrogen bonds       : angle       5.89877 ( 1122)
  Misc. bond           : bond        0.02884 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A  132 THR cc_start: 0.8937 (p) cc_final: 0.8702 (p)
REVERT: A  227 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6501 (mt-10)
REVERT: A  233 ARG cc_start: 0.7535 (mtp-110) cc_final: 0.7269 (mpt180)
REVERT: A  331 SER cc_start: 0.8381 (m) cc_final: 0.8162 (m)
REVERT: A  434 LYS cc_start: 0.8606 (mppt) cc_final: 0.8160 (mmmt)
REVERT: B   95 ARG cc_start: 0.7964 (tpp-160) cc_final: 0.6509 (tpt90)
REVERT: B  285 MET cc_start: 0.7729 (mmt) cc_final: 0.7179 (mmt)
REVERT: C   40 MET cc_start: 0.6571 (tmm) cc_final: 0.6199 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.1204
  time to fit residues: 13.6698
Evaluate side-chains
  76 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.111905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.092293 restraints weight = 9834.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.33
r_work: 0.2950 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.0719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7840  Z= 0.162
  Angle     :  0.555  10.647  10591  Z= 0.290
  Chirality :  0.043   0.129   1169
  Planarity :  0.004   0.039   1360
  Dihedral  :  5.376  72.112   1092
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  6.09 %
    Favored  : 93.54 %
  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 are not related in a simple way.
  whole:  0.59 (0.27), residues: 971
  helix:  1.73 (0.24), residues: 444
  sheet: -0.52 (0.51), residues: 112
  loop : -0.81 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 509 
 TYR   0.018   0.001   TYR A 166 
 PHE   0.015   0.001   PHE A 209 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.004   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 7839)
  covalent geometry    : angle       0.55531 (10591)
  hydrogen bonds       : bond        0.05151 (  391)
  hydrogen bonds       : angle       4.69852 ( 1122)
  Misc. bond           : bond        0.00077 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  233 ARG cc_start: 0.7651 (mtp-110) cc_final: 0.7117 (mpt180)
REVERT: A  331 SER cc_start: 0.8202 (m) cc_final: 0.7948 (m)
REVERT: A  434 LYS cc_start: 0.8794 (mppt) cc_final: 0.8276 (mmmt)
REVERT: B   95 ARG cc_start: 0.7847 (tpp-160) cc_final: 0.6446 (tpt170)
REVERT: B  161 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7250 (ptmt)
REVERT: B  173 MET cc_start: 0.8829 (mtt) cc_final: 0.8399 (mtt)
REVERT: B  244 MET cc_start: 0.8725 (mtt) cc_final: 0.8302 (mtt)
REVERT: B  285 MET cc_start: 0.7790 (mmt) cc_final: 0.7439 (mmt)
REVERT: C   40 MET cc_start: 0.6471 (tmm) cc_final: 0.6130 (tmm)
  outliers start: 3
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1230
  time to fit residues: 12.8377
Evaluate side-chains
  78 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   91 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.112441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.092082 restraints weight = 9780.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3093 rms_B_bonded: 2.38
r_work: 0.2961 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7840  Z= 0.135
  Angle     :  0.505   9.232  10591  Z= 0.263
  Chirality :  0.041   0.127   1169
  Planarity :  0.004   0.038   1360
  Dihedral  :  5.162  72.694   1092
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  8.57 %
    Favored  : 90.68 %
  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 are not related in a simple way.
  whole:  0.90 (0.27), residues: 971
  helix:  1.93 (0.25), residues: 446
  sheet: -0.07 (0.53), residues: 111
  loop : -0.70 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.015   0.001   TYR B 539 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.011   0.001   TRP C  32 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7839)
  covalent geometry    : angle       0.50521 (10591)
  hydrogen bonds       : bond        0.04321 (  391)
  hydrogen bonds       : angle       4.37227 ( 1122)
  Misc. bond           : bond        0.00072 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  233 ARG cc_start: 0.7590 (mtp-110) cc_final: 0.7075 (mpt180)
REVERT: A  331 SER cc_start: 0.8167 (m) cc_final: 0.7915 (m)
REVERT: A  434 LYS cc_start: 0.8798 (mppt) cc_final: 0.8271 (mmmt)
REVERT: B   95 ARG cc_start: 0.7787 (tpp-160) cc_final: 0.6406 (tpt170)
REVERT: B  161 LYS cc_start: 0.8284 (mtmt) cc_final: 0.7301 (ptmm)
REVERT: B  285 MET cc_start: 0.7824 (mmt) cc_final: 0.7534 (mmt)
  outliers start: 6
  outliers final: 4
  residues processed: 87
  average time/residue: 0.1183
  time to fit residues: 13.5359
Evaluate side-chains
  84 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   83 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 42 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 374 HIS
B 135 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.091201 restraints weight = 10086.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.32
r_work: 0.2923 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7840  Z= 0.229
  Angle     :  0.589   9.708  10591  Z= 0.304
  Chirality :  0.045   0.132   1169
  Planarity :  0.004   0.043   1360
  Dihedral  :  5.325  74.375   1092
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.69 %
    Favored  : 88.70 %
  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 are not related in a simple way.
  whole:  0.62 (0.27), residues: 971
  helix:  1.72 (0.24), residues: 445
  sheet: -0.22 (0.52), residues: 111
  loop : -0.86 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 151 
 TYR   0.021   0.002   TYR B 539 
 PHE   0.018   0.002   PHE A 209 
 TRP   0.013   0.001   TRP C  32 
 HIS   0.005   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 7839)
  covalent geometry    : angle       0.58909 (10591)
  hydrogen bonds       : bond        0.05229 (  391)
  hydrogen bonds       : angle       4.43523 ( 1122)
  Misc. bond           : bond        0.00104 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  233 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7123 (mpt180)
REVERT: A  331 SER cc_start: 0.8263 (m) cc_final: 0.8005 (m)
REVERT: A  434 LYS cc_start: 0.8812 (mppt) cc_final: 0.8288 (mmmt)
REVERT: B   95 ARG cc_start: 0.7782 (tpp-160) cc_final: 0.6466 (tpt170)
REVERT: B  161 LYS cc_start: 0.8274 (mtmt) cc_final: 0.7314 (ptmt)
REVERT: B  244 MET cc_start: 0.8844 (mtt) cc_final: 0.8558 (mtt)
REVERT: B  285 MET cc_start: 0.7856 (mmt) cc_final: 0.7590 (mmt)
REVERT: C   40 MET cc_start: 0.6555 (tmm) cc_final: 0.6208 (tmm)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.1105
  time to fit residues: 12.2364
Evaluate side-chains
  83 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  517 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   chunk 85 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.092576 restraints weight = 9941.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.35
r_work: 0.2955 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7840  Z= 0.139
  Angle     :  0.502   8.640  10591  Z= 0.261
  Chirality :  0.042   0.127   1169
  Planarity :  0.004   0.039   1360
  Dihedral  :  5.206  76.753   1092
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  9.81 %
    Favored  : 88.57 %
  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 are not related in a simple way.
  whole:  0.82 (0.27), residues: 971
  helix:  1.92 (0.25), residues: 446
  sheet: -0.07 (0.48), residues: 123
  loop : -0.84 (0.29), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 151 
 TYR   0.012   0.001   TYR B 539 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.002   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7839)
  covalent geometry    : angle       0.50161 (10591)
  hydrogen bonds       : bond        0.04278 (  391)
  hydrogen bonds       : angle       4.27706 ( 1122)
  Misc. bond           : bond        0.00075 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  233 ARG cc_start: 0.7606 (mtp-110) cc_final: 0.7086 (mpt180)
REVERT: A  331 SER cc_start: 0.8157 (m) cc_final: 0.7898 (m)
REVERT: A  434 LYS cc_start: 0.8800 (mppt) cc_final: 0.8276 (mmmt)
REVERT: B   95 ARG cc_start: 0.7757 (tpp-160) cc_final: 0.6414 (tpt170)
REVERT: B  161 LYS cc_start: 0.8257 (mtmt) cc_final: 0.7307 (ptmt)
REVERT: B  244 MET cc_start: 0.8786 (mtt) cc_final: 0.8552 (mtt)
REVERT: C   40 MET cc_start: 0.6511 (tmm) cc_final: 0.6157 (tmm)
  outliers start: 13
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1112
  time to fit residues: 12.3177
Evaluate side-chains
  85 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   91 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 85 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
A 374 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.112287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.092512 restraints weight = 9933.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.35
r_work: 0.2954 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7840  Z= 0.145
  Angle     :  0.500   8.182  10591  Z= 0.260
  Chirality :  0.042   0.126   1169
  Planarity :  0.004   0.038   1360
  Dihedral  :  5.150  76.513   1092
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.68 %
    Favored  : 87.58 %
  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 are not related in a simple way.
  whole:  0.76 (0.27), residues: 971
  helix:  1.97 (0.25), residues: 446
  sheet: -0.45 (0.51), residues: 110
  loop : -0.86 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 151 
 TYR   0.012   0.001   TYR B 539 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.002   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7839)
  covalent geometry    : angle       0.50008 (10591)
  hydrogen bonds       : bond        0.04259 (  391)
  hydrogen bonds       : angle       4.22739 ( 1122)
  Misc. bond           : bond        0.00072 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  233 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7088 (mpt180)
REVERT: A  331 SER cc_start: 0.8156 (m) cc_final: 0.7896 (m)
REVERT: A  434 LYS cc_start: 0.8811 (mppt) cc_final: 0.8288 (mmmt)
REVERT: B   95 ARG cc_start: 0.7727 (tpp-160) cc_final: 0.6394 (tpt170)
REVERT: B  161 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7340 (ptmt)
REVERT: C   40 MET cc_start: 0.6511 (tmm) cc_final: 0.6219 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 87
  average time/residue: 0.1175
  time to fit residues: 13.3851
Evaluate side-chains
  89 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   91 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 85 optimal weight:    0.4980
   chunk 72 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
B 184 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.091495 restraints weight = 10035.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.41
r_work: 0.2947 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7840  Z= 0.150
  Angle     :  0.503   8.199  10591  Z= 0.261
  Chirality :  0.042   0.127   1169
  Planarity :  0.004   0.038   1360
  Dihedral  :  5.143  76.991   1092
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.56 %
    Favored  : 87.45 %
  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 are not related in a simple way.
  whole:  0.76 (0.27), residues: 971
  helix:  1.98 (0.25), residues: 446
  sheet: -0.45 (0.50), residues: 110
  loop : -0.88 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.012   0.001   TYR B 539 
 PHE   0.013   0.001   PHE A 209 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.003   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 7839)
  covalent geometry    : angle       0.50255 (10591)
  hydrogen bonds       : bond        0.04270 (  391)
  hydrogen bonds       : angle       4.20595 ( 1122)
  Misc. bond           : bond        0.00071 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  150 ASP cc_start: 0.7761 (t0) cc_final: 0.7330 (t0)
REVERT: A  233 ARG cc_start: 0.7612 (mtp-110) cc_final: 0.7100 (mpt180)
REVERT: A  331 SER cc_start: 0.8171 (m) cc_final: 0.7903 (m)
REVERT: A  434 LYS cc_start: 0.8818 (mppt) cc_final: 0.8296 (mmmt)
REVERT: B   95 ARG cc_start: 0.7690 (tpp-160) cc_final: 0.6393 (tpt170)
REVERT: B  161 LYS cc_start: 0.8298 (mtmt) cc_final: 0.7333 (ptmt)
REVERT: B  285 MET cc_start: 0.7808 (mmt) cc_final: 0.7472 (mmt)
REVERT: C   40 MET cc_start: 0.6523 (tmm) cc_final: 0.6240 (tmm)
  outliers start: 16
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1116
  time to fit residues: 13.0349
Evaluate side-chains
  87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain B residue   65 GLU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   91 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0370
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0050
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.4272

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
B 542 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.112953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.093352 restraints weight = 9904.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.35
r_work: 0.2983 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7840  Z= 0.107
  Angle     :  0.462   7.580  10591  Z= 0.243
  Chirality :  0.040   0.127   1169
  Planarity :  0.004   0.036   1360
  Dihedral  :  5.012  76.748   1092
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.30 %
    Favored  : 87.33 %
  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 are not related in a simple way.
  whole:  0.95 (0.27), residues: 971
  helix:  2.11 (0.25), residues: 451
  sheet: -0.28 (0.52), residues: 110
  loop : -0.80 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.008   0.001   TYR B 448 
 PHE   0.010   0.001   PHE B 280 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.002   0.001   HIS B 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 7839)
  covalent geometry    : angle       0.46181 (10591)
  hydrogen bonds       : bond        0.03629 (  391)
  hydrogen bonds       : angle       4.12810 ( 1122)
  Misc. bond           : bond        0.00055 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  150 ASP cc_start: 0.7700 (t0) cc_final: 0.7265 (t0)
REVERT: A  233 ARG cc_start: 0.7587 (mtp-110) cc_final: 0.7150 (mpt180)
REVERT: A  331 SER cc_start: 0.8133 (m) cc_final: 0.7896 (m)
REVERT: A  434 LYS cc_start: 0.8782 (mppt) cc_final: 0.8246 (mmmt)
REVERT: B   95 ARG cc_start: 0.7652 (tpp-160) cc_final: 0.6359 (tpt170)
REVERT: B  161 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7331 (ptmt)
REVERT: C   13 MET cc_start: 0.6441 (tpt) cc_final: 0.6234 (mmm)
REVERT: C   40 MET cc_start: 0.6543 (tmm) cc_final: 0.6239 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1095
  time to fit residues: 13.0086
Evaluate side-chains
  84 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain B residue   91 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0050
   chunk 61 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 83 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
B 542 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.113828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.094204 restraints weight = 9815.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.33
r_work: 0.2979 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7840  Z= 0.116
  Angle     :  0.468   7.642  10591  Z= 0.245
  Chirality :  0.041   0.127   1169
  Planarity :  0.004   0.037   1360
  Dihedral  :  4.966  75.815   1092
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.05 %
    Favored  : 86.58 %
  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 are not related in a simple way.
  whole:  1.02 (0.27), residues: 971
  helix:  2.19 (0.25), residues: 446
  sheet: -0.20 (0.52), residues: 110
  loop : -0.77 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.009   0.001   TYR B 448 
 PHE   0.011   0.001   PHE A 209 
 TRP   0.012   0.001   TRP C  32 
 HIS   0.002   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7839)
  covalent geometry    : angle       0.46765 (10591)
  hydrogen bonds       : bond        0.03755 (  391)
  hydrogen bonds       : angle       4.12318 ( 1122)
  Misc. bond           : bond        0.00056 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  150 ASP cc_start: 0.7730 (t0) cc_final: 0.7294 (t0)
REVERT: A  233 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.7084 (mtm-85)
REVERT: A  331 SER cc_start: 0.8128 (m) cc_final: 0.7891 (m)
REVERT: A  434 LYS cc_start: 0.8791 (mppt) cc_final: 0.8258 (mmmt)
REVERT: B   95 ARG cc_start: 0.7628 (tpp-160) cc_final: 0.6364 (tpt170)
REVERT: B  161 LYS cc_start: 0.8264 (mtmt) cc_final: 0.7380 (ptmt)
REVERT: B  285 MET cc_start: 0.7577 (mmt) cc_final: 0.7023 (mmt)
REVERT: C   13 MET cc_start: 0.6468 (tpt) cc_final: 0.6251 (mmm)
REVERT: C   40 MET cc_start: 0.6564 (tmm) cc_final: 0.6259 (tmm)
  outliers start: 11
  outliers final: 10
  residues processed: 85
  average time/residue: 0.1150
  time to fit residues: 12.6516
Evaluate side-chains
  87 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  388 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 73 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
B 542 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.113336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.093609 restraints weight = 9876.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 2.34
r_work: 0.2970 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7840  Z= 0.130
  Angle     :  0.481   7.886  10591  Z= 0.251
  Chirality :  0.041   0.126   1169
  Planarity :  0.004   0.036   1360
  Dihedral  :  4.993  76.191   1092
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.30 %
    Favored  : 86.34 %
  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 are not related in a simple way.
  whole:  0.97 (0.27), residues: 971
  helix:  2.16 (0.25), residues: 445
  sheet: -0.27 (0.51), residues: 110
  loop : -0.78 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.011   0.001   TYR B 448 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.011   0.001   TRP C  32 
 HIS   0.003   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 7839)
  covalent geometry    : angle       0.48123 (10591)
  hydrogen bonds       : bond        0.03925 (  391)
  hydrogen bonds       : angle       4.14188 ( 1122)
  Misc. bond           : bond        0.00059 (    1)

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

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

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1942 Ramachandran restraints generated.
    971 Oldfield, 0 Emsley, 971 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  132 THR cc_start: 0.9082 (p) cc_final: 0.8804 (p)
REVERT: A  150 ASP cc_start: 0.7739 (t0) cc_final: 0.7302 (t0)
REVERT: A  233 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7079 (mtm-85)
REVERT: A  331 SER cc_start: 0.8149 (m) cc_final: 0.7911 (m)
REVERT: A  434 LYS cc_start: 0.8793 (mppt) cc_final: 0.8258 (mmmt)
REVERT: B   95 ARG cc_start: 0.7650 (tpp-160) cc_final: 0.6328 (tpt170)
REVERT: B  161 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7387 (ptmt)
REVERT: B  244 MET cc_start: 0.8849 (mtm) cc_final: 0.8624 (mtt)
REVERT: B  285 MET cc_start: 0.7670 (mmt) cc_final: 0.7096 (mmt)
REVERT: C   40 MET cc_start: 0.6575 (tmm) cc_final: 0.6266 (tmm)
  outliers start: 11
  outliers final: 10
  residues processed: 87
  average time/residue: 0.0982
  time to fit residues: 11.5653
Evaluate side-chains
  88 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  125 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  166 TYR
Chi-restraints excluded: chain A residue  263 LEU
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  472 LEU
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain B residue  388 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 84 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9980
   chunk 75 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
B 542 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.113145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.093380 restraints weight = 9874.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.34
r_work: 0.2970 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7840  Z= 0.132
  Angle     :  0.483   7.935  10591  Z= 0.252
  Chirality :  0.041   0.127   1169
  Planarity :  0.004   0.036   1360
  Dihedral  :  5.007  76.841   1092
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.42 %
    Favored  : 86.09 %
  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 are not related in a simple way.
  whole:  0.97 (0.27), residues: 971
  helix:  2.16 (0.25), residues: 445
  sheet: -0.28 (0.51), residues: 110
  loop : -0.79 (0.28), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.010   0.001   TYR B 448 
 PHE   0.012   0.001   PHE A 209 
 TRP   0.011   0.001   TRP C  32 
 HIS   0.003   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7839)
  covalent geometry    : angle       0.48258 (10591)
  hydrogen bonds       : bond        0.03976 (  391)
  hydrogen bonds       : angle       4.14530 ( 1122)
  Misc. bond           : bond        0.00062 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1894.91 seconds
wall clock time: 33 minutes 11.74 seconds (1991.74 seconds total)