Starting phenix.real_space_refine
on Tue Mar  3 15:28:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lwd_23545/03_2026/7lwd_23545.map"
  }
  resolution = 3.65
  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=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 129 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    4067      2.51       5
     N     975      2.21       5
     O    1087      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 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: 6163
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4319
          Classifications: {'peptide': 541}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 517}
    Chain: "H"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 101
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 3, 68
          Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
      Conformer: "B"
        Number of residues, atoms: 3, 68
          Unusual residues: {'IXX': 1, 'NAG': 1, 'YG7': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          bond proxies already assigned to first conformer: 37
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C08AYG7 A 802 " occ=0.50
      ... (64 atoms not shown)
      pdb=" O02BYG7 A 802 " occ=0.50
  Time building chain proxies: 1.33, per 1000 atoms: 0.22
  Number of scatterers: 6163
  At special positions: 0
  Unit cell: (84.888, 73.872, 116.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1087      8.00
     N     975      7.00
     C    4067      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 253.5 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1402

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 7 sheets defined
      53.2% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.729A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   SER A  91 " --> pdb=" O   ASP A  87 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A  93 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A  97 " --> pdb=" O   ILE A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 5.212A  pdb=" N   PHE A 105 " --> pdb=" O   ASN A 101 " (cutoff:3.500A)
      Proline residue:  A 106  - end of helix
      removed outlier: 3.737A  pdb=" N   GLN A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ASN A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 129
      removed outlier: 3.745A  pdb=" N   MET A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   PHE A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 150 through 155
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 159 through 189
      removed outlier: 4.284A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   MET A 180 " --> pdb=" O   TYR A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 270
      removed outlier: 3.855A  pdb=" N   CYS A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   MET A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 262 " --> pdb=" O   CYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 285
    Processing helix  chain 'A' and resid 286 through 302
      removed outlier: 3.762A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 4.174A  pdb=" N   PHE A 311 " --> pdb=" O   ARG A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 321
      removed outlier: 3.756A  pdb=" N   LEU A 320 " --> pdb=" O   ASN A 316 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A 321 " --> pdb=" O   TRP A 317 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 316 through 321'
    Processing helix  chain 'A' and resid 322 through 338
      removed outlier: 4.327A  pdb=" N   TRP A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 349
    Processing helix  chain 'A' and resid 360 through 390
      removed outlier: 3.512A  pdb=" N   THR A 364 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   SER A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   VAL A 366 " --> pdb=" O   LEU A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 408
    Processing helix  chain 'A' and resid 408 through 417
    Processing helix  chain 'A' and resid 424 through 454
      removed outlier: 3.844A  pdb=" N   GLY A 435 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ASP A 437 " --> pdb=" O   THR A 433 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   SER A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 477
    Processing helix  chain 'A' and resid 485 through 494
      removed outlier: 4.296A  pdb=" N   LEU A 491 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
      removed outlier: 3.723A  pdb=" N   LEU A 502 " --> pdb=" O   GLY A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 3.972A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 544
      removed outlier: 4.483A  pdb=" N   VAL A 542 " --> pdb=" O   ARG A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
      removed outlier: 3.539A  pdb=" N   LEU A 550 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   PHE A 556 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 585
      removed outlier: 3.668A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 572 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.810A  pdb=" N   ILE A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   THR A 600 " --> pdb=" O   ARG A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 611
      removed outlier: 4.137A  pdb=" N   SER A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 3.612A  pdb=" N   TYR H  50 " --> pdb=" O   ARG H  47 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   SER H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 47 through 51'
    Processing helix  chain 'H' and resid 82 through 86
    Processing helix  chain 'H' and resid 106 through 110
      removed outlier: 3.621A  pdb=" N   SER H 110 " --> pdb=" O   SER H 107 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 120 through 124
    Processing sheet with id=AA1, first strand: chain 'H' and resid 29 through 30
      removed outlier: 6.369A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 137 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'H' and resid 38 through 42
      removed outlier: 3.648A  pdb=" N   ILE H  39 " --> pdb=" O   MET H 100 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR H  88 " --> pdb=" O   GLN H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 78 through 79
      removed outlier: 6.914A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL H 112 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 24 through 27
      removed outlier: 3.545A  pdb=" N   SER L  27 " --> pdb=" O   SER L  42 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TYR L  94 " --> pdb=" O   SER L  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51
      removed outlier: 3.885A  pdb=" N   ASN L  51 " --> pdb=" O   ILE L  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 77 through 78
      removed outlier: 6.536A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   TYR L  73 " --> pdb=" O   LEU L  57 " (cutoff:3.500A)
      removed outlier: 6.910A  pdb=" N   LEU L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    759 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 926
        1.25 -     1.39: 1706
        1.39 -     1.53: 3326
        1.53 -     1.67: 346
        1.67 -     1.81: 49
  Bond restraints: 6353
  Sorted by residual:
  bond pdb=" C23AYG7 A 802 "
       pdb=" O01AYG7 A 802 "
    ideal  model  delta    sigma   weight residual
    1.351  1.588 -0.237 2.00e-02 2.50e+03 1.40e+02
  bond pdb=" C23BYG7 A 802 "
       pdb=" O01BYG7 A 802 "
    ideal  model  delta    sigma   weight residual
    1.351  1.587 -0.236 2.00e-02 2.50e+03 1.39e+02
  bond pdb=" C21BYG7 A 802 "
       pdb=" C26BYG7 A 802 "
    ideal  model  delta    sigma   weight residual
    1.432  1.224  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C21AYG7 A 802 "
       pdb=" C26AYG7 A 802 "
    ideal  model  delta    sigma   weight residual
    1.432  1.226  0.206 2.00e-02 2.50e+03 1.06e+02
  bond pdb=" C26BYG7 A 802 "
       pdb=" C29BYG7 A 802 "
    ideal  model  delta    sigma   weight residual
    1.354  1.171  0.183 2.00e-02 2.50e+03 8.38e+01
  ... (remaining 6348 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.98: 8569
        3.98 -     7.95: 55
        7.95 -    11.93: 23
       11.93 -    15.91: 2
       15.91 -    19.89: 4
  Bond angle restraints: 8653
  Sorted by residual:
  angle pdb=" C26BYG7 A 802 "
        pdb=" C29BYG7 A 802 "
        pdb=" O01BYG7 A 802 "
      ideal   model   delta    sigma   weight residual
     111.69  131.58  -19.89 3.00e+00 1.11e-01 4.39e+01
  angle pdb=" C26AYG7 A 802 "
        pdb=" C29AYG7 A 802 "
        pdb=" O01AYG7 A 802 "
      ideal   model   delta    sigma   weight residual
     111.69  131.49  -19.80 3.00e+00 1.11e-01 4.36e+01
  angle pdb=" C23BYG7 A 802 "
        pdb=" O01BYG7 A 802 "
        pdb=" C29BYG7 A 802 "
      ideal   model   delta    sigma   weight residual
     106.53   88.85   17.68 3.00e+00 1.11e-01 3.47e+01
  angle pdb=" C23AYG7 A 802 "
        pdb=" O01AYG7 A 802 "
        pdb=" C29AYG7 A 802 "
      ideal   model   delta    sigma   weight residual
     106.53   88.98   17.55 3.00e+00 1.11e-01 3.42e+01
  angle pdb=" C   GLU L  47 "
        pdb=" N   SER L  48 "
        pdb=" CA  SER L  48 "
      ideal   model   delta    sigma   weight residual
     121.70  131.48   -9.78 1.80e+00 3.09e-01 2.95e+01
  ... (remaining 8648 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.23: 3530
       33.23 -    66.46: 74
       66.46 -    99.69: 10
       99.69 -   132.92: 6
      132.92 -   166.15: 2
  Dihedral angle restraints: 3622
    sinusoidal: 1412
      harmonic: 2210
  Sorted by residual:
  dihedral pdb=" CB  CYS A 200 "
           pdb=" SG  CYS A 200 "
           pdb=" SG  CYS A 209 "
           pdb=" CB  CYS A 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  142.29  -49.29     1      1.00e+01 1.00e-02 3.34e+01
  dihedral pdb=" C13BYG7 A 802 "
           pdb=" C14BYG7 A 802 "
           pdb=" C16BYG7 A 802 "
           pdb=" C17BYG7 A 802 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.61  103.54 -166.15     1      3.00e+01 1.11e-03 2.10e+01
  dihedral pdb=" CA  GLU L  47 "
           pdb=" C   GLU L  47 "
           pdb=" N   SER L  48 "
           pdb=" CA  SER L  48 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   22.50  -22.50     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 3619 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 546
       0.031 -    0.061: 283
       0.061 -    0.092: 78
       0.092 -    0.122: 30
       0.122 -    0.153: 1
  Chirality restraints: 938
  Sorted by residual:
  chirality pdb=" CA  PHE A 380 "
            pdb=" N   PHE A 380 "
            pdb=" C   PHE A 380 "
            pdb=" CB  PHE A 380 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.84e-01
  chirality pdb=" CA  ILE L  41 "
            pdb=" N   ILE L  41 "
            pdb=" C   ILE L  41 "
            pdb=" CB  ILE L  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.57e-01
  chirality pdb=" CA  TRP A 103 "
            pdb=" N   TRP A 103 "
            pdb=" C   TRP A 103 "
            pdb=" CB  TRP A 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.52e-01
  ... (remaining 935 not shown)

  Planarity restraints: 1060
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 465 "    0.014 2.00e-02 2.50e+03   2.76e-02 7.59e+00
        pdb=" C   PHE A 465 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   PHE A 465 "    0.018 2.00e-02 2.50e+03
        pdb=" N   VAL A 466 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 103 "    0.014 2.00e-02 2.50e+03   1.14e-02 3.25e+00
        pdb=" CG  TRP A 103 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 103 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 103 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 103 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 103 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 287 "    0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO A 288 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 288 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 288 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1057 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 50
        2.60 -     3.17: 5503
        3.17 -     3.75: 9620
        3.75 -     4.32: 13443
        4.32 -     4.90: 22109
  Nonbonded interactions: 50725
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 208 "
            pdb=" C1  NAG A 803 "
     model   vdw
     2.024 3.550
  nonbonded pdb=" OG  SER A 199 "
            pdb=" OD2 ASP H  74 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" ND2 ASN A 208 "
            pdb=" C2  NAG A 803 "
     model   vdw
     2.225 3.550
  nonbonded pdb=" OH  TYR A 185 "
            pdb=" OE1 GLN A 254 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NE2 GLN H  25 "
            pdb=" OG1 THR H 134 "
     model   vdw
     2.326 3.120
  ... (remaining 50720 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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
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      :  0.011   0.237   6356  Z= 0.527
  Angle     :  0.972  19.885   8659  Z= 0.406
  Chirality :  0.039   0.153    938
  Planarity :  0.004   0.036   1060
  Dihedral  : 16.267 166.146   2211
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -4.15 (0.25), residues: 763
  helix: -1.97 (0.23), residues: 353
  sheet: -4.04 (0.39), residues: 93
  loop : -3.15 (0.30), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  69 
 TYR   0.014   0.001   TYR A 186 
 PHE   0.024   0.001   PHE A 287 
 TRP   0.031   0.001   TRP A 103 
 HIS   0.001   0.000   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.01059 ( 6353)
  covalent geometry    : angle       0.97237 ( 8653)
  SS BOND              : bond        0.00570 (    3)
  SS BOND              : angle       0.36361 (    6)
  hydrogen bonds       : bond        0.15745 (  265)
  hydrogen bonds       : angle       6.88862 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 MET cc_start: 0.7891 (tpp) cc_final: 0.7537 (tpp)
REVERT: A  201 LYS cc_start: 0.6290 (mmtt) cc_final: 0.5828 (tttm)
REVERT: A  595 TYR cc_start: 0.7996 (t80) cc_final: 0.7562 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0735
  time to fit residues: 12.7928
Evaluate side-chains
  105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 177 ASN
A 208 ASN
A 368 ASN
A 416 ASN
L  62 GLN
L  78 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.181433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.160525 restraints weight = 7801.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.164488 restraints weight = 4826.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167086 restraints weight = 3448.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.168644 restraints weight = 2711.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.169622 restraints weight = 2300.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.169         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6356  Z= 0.125
  Angle     :  0.573   9.542   8659  Z= 0.292
  Chirality :  0.041   0.149    938
  Planarity :  0.004   0.047   1060
  Dihedral  : 11.443 177.088    894
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.49 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -2.89 (0.29), residues: 763
  helix: -0.98 (0.26), residues: 358
  sheet: -3.38 (0.47), residues: 86
  loop : -2.51 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 104 
 TYR   0.016   0.001   TYR A 312 
 PHE   0.019   0.001   PHE A 586 
 TRP   0.022   0.001   TRP A 103 
 HIS   0.001   0.000   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6353)
  covalent geometry    : angle       0.57214 ( 8653)
  SS BOND              : bond        0.00830 (    3)
  SS BOND              : angle       1.29470 (    6)
  hydrogen bonds       : bond        0.03377 (  265)
  hydrogen bonds       : angle       5.19065 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8244 (t80) cc_final: 0.8002 (t80)
REVERT: A  201 LYS cc_start: 0.6507 (mmtt) cc_final: 0.6143 (mmtp)
REVERT: A  386 MET cc_start: 0.7641 (mtp) cc_final: 0.7318 (mtp)
REVERT: A  392 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6792 (tm-30)
REVERT: A  595 TYR cc_start: 0.7964 (t80) cc_final: 0.7654 (t80)
  outliers start: 7
  outliers final: 2
  residues processed: 117
  average time/residue: 0.0729
  time to fit residues: 11.5587
Evaluate side-chains
  104 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain L residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0670
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 416 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.178882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157851 restraints weight = 7641.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.161731 restraints weight = 4784.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.164295 restraints weight = 3449.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.165912 restraints weight = 2728.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.167233 restraints weight = 2308.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3931
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3931 r_free = 0.3931    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6356  Z= 0.137
  Angle     :  0.572   9.496   8659  Z= 0.292
  Chirality :  0.040   0.157    938
  Planarity :  0.004   0.039   1060
  Dihedral  : 10.562 172.897    894
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.74 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -2.38 (0.30), residues: 763
  helix: -0.57 (0.27), residues: 357
  sheet: -3.03 (0.47), residues: 90
  loop : -2.24 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 152 
 TYR   0.017   0.001   TYR A 312 
 PHE   0.017   0.001   PHE A 380 
 TRP   0.021   0.001   TRP A 103 
 HIS   0.001   0.000   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6353)
  covalent geometry    : angle       0.57196 ( 8653)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       1.09668 (    6)
  hydrogen bonds       : bond        0.03289 (  265)
  hydrogen bonds       : angle       4.94500 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.6898 (mmtt) cc_final: 0.6343 (mmtp)
REVERT: A  386 MET cc_start: 0.7660 (mtp) cc_final: 0.7438 (mtp)
REVERT: A  595 TYR cc_start: 0.7943 (t80) cc_final: 0.7716 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 113
  average time/residue: 0.0676
  time to fit residues: 10.6366
Evaluate side-chains
  107 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  583 THR
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 40 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 456 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.179277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.155635 restraints weight = 13858.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.161644 restraints weight = 8128.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.162660 restraints weight = 4517.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165434 restraints weight = 3546.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.168345 restraints weight = 2608.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3948 r_free = 0.3948    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3947 r_free = 0.3947    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6356  Z= 0.131
  Angle     :  0.553   9.523   8659  Z= 0.283
  Chirality :  0.040   0.160    938
  Planarity :  0.004   0.035   1060
  Dihedral  : 10.415 172.250    894
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.83 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -2.05 (0.30), residues: 763
  helix: -0.34 (0.27), residues: 358
  sheet: -3.04 (0.48), residues: 79
  loop : -2.02 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 117 
 TYR   0.023   0.001   TYR H  79 
 PHE   0.018   0.001   PHE A 380 
 TRP   0.039   0.001   TRP A 103 
 HIS   0.008   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6353)
  covalent geometry    : angle       0.55298 ( 8653)
  SS BOND              : bond        0.00288 (    3)
  SS BOND              : angle       0.94886 (    6)
  hydrogen bonds       : bond        0.03201 (  265)
  hydrogen bonds       : angle       4.84160 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 TYR cc_start: 0.8171 (t80) cc_final: 0.7937 (t80)
REVERT: A  142 TYR cc_start: 0.8308 (t80) cc_final: 0.8099 (t80)
REVERT: A  201 LYS cc_start: 0.6941 (mmtt) cc_final: 0.6392 (mmtp)
REVERT: A  386 MET cc_start: 0.7639 (mtp) cc_final: 0.7369 (mtp)
REVERT: A  595 TYR cc_start: 0.7958 (t80) cc_final: 0.7627 (t80)
  outliers start: 16
  outliers final: 8
  residues processed: 116
  average time/residue: 0.0661
  time to fit residues: 10.7075
Evaluate side-chains
  109 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    0.4980
   chunk 34 optimal weight:    0.2980
   chunk 41 optimal weight:    0.0370
   chunk 51 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A 456 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.161134 restraints weight = 8700.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165244 restraints weight = 5189.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168116 restraints weight = 3659.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.169970 restraints weight = 2826.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.171385 restraints weight = 2339.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3973 r_free = 0.3973    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3973 r_free = 0.3973    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6356  Z= 0.113
  Angle     :  0.545   9.480   8659  Z= 0.281
  Chirality :  0.040   0.210    938
  Planarity :  0.004   0.037   1060
  Dihedral  : 10.275 173.753    894
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.90 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 19.38 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.68 (0.30), residues: 763
  helix: -0.06 (0.28), residues: 351
  sheet: -2.85 (0.49), residues: 77
  loop : -1.77 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  47 
 TYR   0.015   0.001   TYR H  79 
 PHE   0.017   0.001   PHE A 380 
 TRP   0.027   0.001   TRP A 103 
 HIS   0.008   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 6353)
  covalent geometry    : angle       0.54502 ( 8653)
  SS BOND              : bond        0.00196 (    3)
  SS BOND              : angle       0.67326 (    6)
  hydrogen bonds       : bond        0.03064 (  265)
  hydrogen bonds       : angle       4.72577 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 TYR cc_start: 0.8239 (t80) cc_final: 0.7842 (t80)
REVERT: A  201 LYS cc_start: 0.6879 (mmtt) cc_final: 0.6307 (mmtp)
REVERT: A  386 MET cc_start: 0.7503 (mtp) cc_final: 0.7246 (mtp)
REVERT: A  544 ILE cc_start: 0.9131 (mm) cc_final: 0.8892 (mt)
REVERT: A  595 TYR cc_start: 0.7929 (t80) cc_final: 0.7613 (t80)
REVERT: H   37 VAL cc_start: 0.8904 (p) cc_final: 0.8594 (m)
  outliers start: 13
  outliers final: 7
  residues processed: 112
  average time/residue: 0.0706
  time to fit residues: 10.8991
Evaluate side-chains
  105 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue  107 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 66 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    0.3980
   chunk 3 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   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 456 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.175964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.153656 restraints weight = 8240.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.157523 restraints weight = 5173.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.160122 restraints weight = 3738.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161647 restraints weight = 2966.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.162968 restraints weight = 2539.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3856 r_free = 0.3856    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3856 r_free = 0.3856    target_work(ls_wunit_k1) = 0.160         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6356  Z= 0.141
  Angle     :  0.564   9.589   8659  Z= 0.293
  Chirality :  0.040   0.161    938
  Planarity :  0.004   0.038   1060
  Dihedral  : 10.193 171.285    894
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 21.09 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.71 (0.30), residues: 763
  helix: -0.15 (0.27), residues: 361
  sheet: -2.64 (0.50), residues: 76
  loop : -1.82 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  47 
 TYR   0.018   0.001   TYR A 134 
 PHE   0.019   0.001   PHE A 380 
 TRP   0.021   0.001   TRP A 103 
 HIS   0.007   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6353)
  covalent geometry    : angle       0.56363 ( 8653)
  SS BOND              : bond        0.00249 (    3)
  SS BOND              : angle       0.69716 (    6)
  hydrogen bonds       : bond        0.03197 (  265)
  hydrogen bonds       : angle       4.78656 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7087 (mmtt) cc_final: 0.6429 (mmtp)
REVERT: A  386 MET cc_start: 0.7664 (mtp) cc_final: 0.7394 (mtp)
REVERT: A  595 TYR cc_start: 0.8008 (t80) cc_final: 0.7710 (t80)
REVERT: A  610 LYS cc_start: 0.9096 (tptp) cc_final: 0.8881 (tptt)
REVERT: H   37 VAL cc_start: 0.8945 (p) cc_final: 0.8649 (m)
REVERT: L   66 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.7172 (mp10)
  outliers start: 16
  outliers final: 11
  residues processed: 114
  average time/residue: 0.0654
  time to fit residues: 10.4558
Evaluate side-chains
  115 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   66 GLN
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    0.3980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9980
   chunk 64 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 28 optimal weight:    0.4980
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 456 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.146710 restraints weight = 10736.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.151014 restraints weight = 6303.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.154051 restraints weight = 4412.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.156070 restraints weight = 3424.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.157522 restraints weight = 2863.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3784 r_free = 0.3784    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3784 r_free = 0.3784    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6356  Z= 0.120
  Angle     :  0.564   9.512   8659  Z= 0.287
  Chirality :  0.040   0.236    938
  Planarity :  0.004   0.040   1060
  Dihedral  : 10.157 172.102    894
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.62 %
    Favored  : 76.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.48 (0.31), residues: 763
  helix: -0.00 (0.28), residues: 357
  sheet: -2.53 (0.50), residues: 76
  loop : -1.62 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  47 
 TYR   0.017   0.001   TYR A 134 
 PHE   0.019   0.001   PHE A 380 
 TRP   0.019   0.001   TRP A 103 
 HIS   0.007   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 6353)
  covalent geometry    : angle       0.56421 ( 8653)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.62780 (    6)
  hydrogen bonds       : bond        0.03111 (  265)
  hydrogen bonds       : angle       4.70309 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7862 (OUTLIER) cc_final: 0.7614 (t0)
REVERT: A  201 LYS cc_start: 0.7040 (mmtt) cc_final: 0.6394 (mmtp)
REVERT: A  386 MET cc_start: 0.7627 (mtp) cc_final: 0.7349 (mtp)
REVERT: A  547 LEU cc_start: 0.8829 (tt) cc_final: 0.8534 (tp)
REVERT: A  595 TYR cc_start: 0.7967 (t80) cc_final: 0.7654 (t80)
REVERT: H   37 VAL cc_start: 0.8957 (p) cc_final: 0.8668 (m)
REVERT: L   66 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7129 (mp10)
  outliers start: 21
  outliers final: 14
  residues processed: 120
  average time/residue: 0.0665
  time to fit residues: 11.1151
Evaluate side-chains
  115 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   66 GLN
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain L residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 68 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 26 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   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 416 ASN
A 456 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.170378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.144034 restraints weight = 11520.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.149874 restraints weight = 7230.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.151903 restraints weight = 4236.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.155608 restraints weight = 3222.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.156021 restraints weight = 2609.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3769
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3769 r_free = 0.3769    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3769
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6356  Z= 0.138
  Angle     :  0.606  12.007   8659  Z= 0.308
  Chirality :  0.041   0.209    938
  Planarity :  0.004   0.040   1060
  Dihedral  : 10.150 171.453    894
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 22.02 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.55 (0.30), residues: 763
  helix: -0.07 (0.28), residues: 359
  sheet: -2.47 (0.50), residues: 76
  loop : -1.68 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 117 
 TYR   0.016   0.001   TYR A 134 
 PHE   0.019   0.001   PHE A 380 
 TRP   0.018   0.001   TRP A 103 
 HIS   0.007   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 6353)
  covalent geometry    : angle       0.60558 ( 8653)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.47971 (    6)
  hydrogen bonds       : bond        0.03184 (  265)
  hydrogen bonds       : angle       4.70010 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6635 (mmmt)
REVERT: A  386 MET cc_start: 0.7623 (mtp) cc_final: 0.7310 (mtp)
REVERT: A  547 LEU cc_start: 0.8834 (tt) cc_final: 0.8547 (tp)
REVERT: A  595 TYR cc_start: 0.7950 (t80) cc_final: 0.7613 (t80)
REVERT: H   37 VAL cc_start: 0.8986 (p) cc_final: 0.8689 (m)
REVERT: L   66 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.7144 (mp10)
  outliers start: 16
  outliers final: 14
  residues processed: 113
  average time/residue: 0.0581
  time to fit residues: 9.3143
Evaluate side-chains
  117 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain A residue  565 LEU
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   66 GLN
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain L residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 456 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.169028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.145697 restraints weight = 8427.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.149383 restraints weight = 5399.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.151799 restraints weight = 3967.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.153620 restraints weight = 3202.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.154655 restraints weight = 2742.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6356  Z= 0.148
  Angle     :  0.608  11.462   8659  Z= 0.310
  Chirality :  0.042   0.214    938
  Planarity :  0.004   0.042   1060
  Dihedral  : 10.141 169.295    894
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.48 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.56 (0.30), residues: 763
  helix: -0.10 (0.27), residues: 359
  sheet: -2.51 (0.50), residues: 70
  loop : -1.68 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 117 
 TYR   0.019   0.001   TYR A 134 
 PHE   0.020   0.001   PHE A 380 
 TRP   0.018   0.001   TRP A 103 
 HIS   0.006   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6353)
  covalent geometry    : angle       0.60819 ( 8653)
  SS BOND              : bond        0.00246 (    3)
  SS BOND              : angle       0.57146 (    6)
  hydrogen bonds       : bond        0.03290 (  265)
  hydrogen bonds       : angle       4.72485 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
REVERT: A  145 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7720 (t0)
REVERT: A  201 LYS cc_start: 0.7322 (mmtt) cc_final: 0.6635 (mmtp)
REVERT: A  386 MET cc_start: 0.7630 (mtp) cc_final: 0.7341 (mtp)
REVERT: A  547 LEU cc_start: 0.8819 (tt) cc_final: 0.8532 (tp)
REVERT: A  605 LYS cc_start: 0.8455 (tppt) cc_final: 0.8236 (tppt)
REVERT: H   37 VAL cc_start: 0.8966 (p) cc_final: 0.8676 (m)
REVERT: L   66 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7189 (mp10)
  outliers start: 17
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0559
  time to fit residues: 9.3920
Evaluate side-chains
  114 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ASN
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  269 SER
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   66 GLN
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain L residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 11 optimal weight:    0.2980
   chunk 30 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0870
   chunk 48 optimal weight:    0.0030
   overall best weight:    0.2568

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 456 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.173743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.148807 restraints weight = 8989.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.152913 restraints weight = 5575.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155776 restraints weight = 4038.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.157657 restraints weight = 3205.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.159121 restraints weight = 2713.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3808
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3808 r_free = 0.3808    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3808
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6356  Z= 0.112
  Angle     :  0.589  11.342   8659  Z= 0.302
  Chirality :  0.041   0.256    938
  Planarity :  0.004   0.041   1060
  Dihedral  : 10.050 172.354    894
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 23.57 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.35 (0.30), residues: 763
  helix:  0.08 (0.28), residues: 355
  sheet: -2.43 (0.49), residues: 73
  loop : -1.55 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 144 
 TYR   0.018   0.001   TYR A 134 
 PHE   0.018   0.001   PHE A 380 
 TRP   0.021   0.001   TRP A 103 
 HIS   0.004   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 6353)
  covalent geometry    : angle       0.58873 ( 8653)
  SS BOND              : bond        0.00127 (    3)
  SS BOND              : angle       0.45893 (    6)
  hydrogen bonds       : bond        0.03081 (  265)
  hydrogen bonds       : angle       4.59918 (  759)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6655 (mmtp)
REVERT: A  344 LEU cc_start: 0.7860 (mt) cc_final: 0.7650 (mt)
REVERT: A  386 MET cc_start: 0.7596 (mtp) cc_final: 0.7270 (mtp)
REVERT: A  544 ILE cc_start: 0.9155 (mm) cc_final: 0.8904 (mt)
REVERT: H   37 VAL cc_start: 0.8937 (p) cc_final: 0.8643 (m)
REVERT: L   66 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7097 (mp10)
  outliers start: 15
  outliers final: 12
  residues processed: 108
  average time/residue: 0.0546
  time to fit residues: 8.4225
Evaluate side-chains
  108 residues out of total 645 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ILE
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  274 VAL
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  392 GLU
Chi-restraints excluded: chain A residue  409 THR
Chi-restraints excluded: chain H residue   90 THR
Chi-restraints excluded: chain L residue   66 GLN
Chi-restraints excluded: chain L residue  107 THR
Chi-restraints excluded: chain L residue  118 VAL
Chi-restraints excluded: chain L residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0670
   chunk 8 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.4130

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
A 208 ASN
A 456 HIS
** H  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.173327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.147354 restraints weight = 11210.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.151811 restraints weight = 6994.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.155280 restraints weight = 4352.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.156720 restraints weight = 3275.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.157521 restraints weight = 2993.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3786 r_free = 0.3786    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6356  Z= 0.120
  Angle     :  0.609  12.717   8659  Z= 0.307
  Chirality :  0.041   0.275    938
  Planarity :  0.004   0.042   1060
  Dihedral  :  9.997 172.848    894
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 23.72 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.27 %
    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: -1.41 (0.30), residues: 763
  helix:  0.06 (0.28), residues: 357
  sheet: -2.48 (0.52), residues: 68
  loop : -1.64 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 144 
 TYR   0.018   0.001   TYR A 134 
 PHE   0.016   0.001   PHE A 380 
 TRP   0.022   0.001   TRP A 103 
 HIS   0.004   0.001   HIS A 456 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6353)
  covalent geometry    : angle       0.60909 ( 8653)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       0.52714 (    6)
  hydrogen bonds       : bond        0.03065 (  265)
  hydrogen bonds       : angle       4.61017 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1286.17 seconds
wall clock time: 22 minutes 48.63 seconds (1368.63 seconds total)