Starting phenix.real_space_refine
on Tue Aug  4 22:27:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/08_2026/9d85_46630_neut.cif"
  }
  resolution = 3.59
  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=   0.000 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      65      5.49       5
     S      27      5.16       5
     C    4342      2.51       5
     N    1229      2.21       5
     O    1538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7201
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 1585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1585
          Classifications: {'peptide': 191}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 188}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1114
          Classifications: {'peptide': 145}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 2, 'TRANS': 142}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 40
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 34
    Chain: "K"
      Number of atoms: 2502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2502
          Classifications: {'peptide': 327}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 310}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "P"
      Number of atoms: 615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 615
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "T"
      Number of atoms: 1385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 1385
          Classifications: {'RNA': 65}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 28, 'rna3p_pyr': 23}
          Link IDs: {'rna2p': 14, 'rna3p': 50}
          Chain breaks: 3
  Time building chain proxies: 1.79, per 1000 atoms: 0.25
  Number of scatterers: 7201
  At special positions: 0
  Unit cell: (70.04, 89.61, 130.81, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P      65     15.00
     O    1538      8.00
     N    1229      7.00
     C    4342      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Atom "ATOM   5823  O4'   G T   1 .*.     O  " rejected from bonding due to valence issues.
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 380.1 milliseconds
  

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1380

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      53.5% alpha, 14.7% beta
      13 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 369 through 391
    Processing helix  chain 'B' and resid 392 through 395
    Processing helix  chain 'B' and resid 421 through 426
      removed outlier: 4.443A  pdb=" N   GLU B 426 " --> pdb=" O   LYS B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 445
      removed outlier: 3.817A  pdb=" N   TYR B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS B 441 " --> pdb=" O   GLU B 437 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   LEU B 442 " --> pdb=" O   ILE B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 496
      removed outlier: 3.771A  pdb=" N   LYS B 480 " --> pdb=" O   LEU B 476 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 514
    Processing helix  chain 'B' and resid 516 through 529
      removed outlier: 3.964A  pdb=" N   ILE B 520 " --> pdb=" O   ARG B 516 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS B 525 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ASP B 526 " --> pdb=" O   GLU B 522 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 18 through 23
      removed outlier: 4.125A  pdb=" N   ASN C  22 " --> pdb=" O   ASN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 51
    Processing helix  chain 'C' and resid 57 through 68
      removed outlier: 4.094A  pdb=" N   LEU C  63 " --> pdb=" O   TRP C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 80
      removed outlier: 3.598A  pdb=" N   ALA C  75 " --> pdb=" O   GLN C  71 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   LYS C  77 " --> pdb=" O   HIS C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 104
    Processing helix  chain 'C' and resid 109 through 113
    Processing helix  chain 'C' and resid 115 through 124
    Processing helix  chain 'C' and resid 133 through 144
    Processing helix  chain 'K' and resid 45 through 63
      Proline residue:  K  53  - end of helix
    Processing helix  chain 'K' and resid 79 through 98
    Processing helix  chain 'K' and resid 106 through 118
      removed outlier: 3.747A  pdb=" N   ILE K 111 " --> pdb=" O   CYS K 107 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 153 through 166
    Processing helix  chain 'K' and resid 170 through 179
      removed outlier: 4.339A  pdb=" N   TYR K 174 " --> pdb=" O   PRO K 170 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 199 through 212
    Processing helix  chain 'K' and resid 215 through 243
    Processing helix  chain 'K' and resid 251 through 255
    Processing helix  chain 'K' and resid 256 through 270
      removed outlier: 3.961A  pdb=" N   ARG K 260 " --> pdb=" O   ASN K 256 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 278 through 283
      removed outlier: 3.623A  pdb=" N   GLY K 283 " --> pdb=" O   LYS K 279 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 285 through 299
      removed outlier: 4.250A  pdb=" N   ILE K 289 " --> pdb=" O   ASN K 285 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ASN K 299 " --> pdb=" O   LEU K 295 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 304 through 308
    Processing helix  chain 'K' and resid 315 through 319
      removed outlier: 3.571A  pdb=" N   VAL K 319 " --> pdb=" O   THR K 316 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 16 through 32
      removed outlier: 4.095A  pdb=" N   TYR P  29 " --> pdb=" O   GLU P  25 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLU P  30 " --> pdb=" O   ALA P  26 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 58 through 80
      removed outlier: 3.833A  pdb=" N   ILE P  80 " --> pdb=" O   ALA P  76 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 346 through 351
    Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 420
    Processing sheet with id=AA3, first strand: chain 'B' and resid 447 through 449
    Processing sheet with id=AA4, first strand: chain 'C' and resid 28 through 30
    Processing sheet with id=AA5, first strand: chain 'K' and resid 23 through 31
      removed outlier: 3.525A  pdb=" N   GLU K  23 " --> pdb=" O   THR K  19 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ILE K  17 " --> pdb=" O   LEU K  25 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   ASN K  27 " --> pdb=" O   VAL K  15 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   VAL K  15 " --> pdb=" O   ASN K  27 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   THR K  29 " --> pdb=" O   THR K  13 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   THR K  13 " --> pdb=" O   THR K  29 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ILE K  71 " --> pdb=" O   ILE K 102 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   VAL K 104 " --> pdb=" O   ILE K  71 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE K  73 " --> pdb=" O   VAL K 104 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 143 through 148
      removed outlier: 6.527A  pdb=" N   VAL K 135 " --> pdb=" O   PHE K 146 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   GLU K 148 " --> pdb=" O   THR K 133 " (cutoff:3.500A)
      removed outlier: 7.805A  pdb=" N   THR K 133 " --> pdb=" O   GLU K 148 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   LEU K 124 " --> pdb=" O   MET K 248 " (cutoff:3.500A)
      removed outlier: 7.381A  pdb=" N   VAL K 250 " --> pdb=" O   LEU K 124 " (cutoff:3.500A)
      removed outlier: 5.876A  pdb=" N   LEU K 126 " --> pdb=" O   VAL K 250 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL K 247 " --> pdb=" O   ASP K 273 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'K' and resid 192 through 193
      removed outlier: 3.669A  pdb=" N   LYS K 193 " --> pdb=" O   ASP K 196 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'P' and resid 7 through 13

    324 hydrogen bonds defined for protein.
    918 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      33 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 0.90

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1430
        1.33 -     1.45: 1919
        1.45 -     1.57: 3937
        1.57 -     1.69: 126
        1.69 -     1.81: 46
  Bond restraints: 7458
  Sorted by residual:
  bond pdb=" P     U T  44 "
       pdb=" O5'   U T  44 "
    ideal  model  delta    sigma   weight residual
    1.593  1.632 -0.039 1.00e-02 1.00e+04 1.50e+01
  bond pdb=" P     G T  45 "
       pdb=" O5'   G T  45 "
    ideal  model  delta    sigma   weight residual
    1.593  1.631 -0.038 1.00e-02 1.00e+04 1.45e+01
  bond pdb=" P     G T  42 "
       pdb=" O5'   G T  42 "
    ideal  model  delta    sigma   weight residual
    1.593  1.629 -0.036 1.00e-02 1.00e+04 1.33e+01
  bond pdb=" CA  PRO K  34 "
       pdb=" C   PRO K  34 "
    ideal  model  delta    sigma   weight residual
    1.517  1.549 -0.032 9.30e-03 1.16e+04 1.21e+01
  bond pdb=" N   GLN K  37 "
       pdb=" CA  GLN K  37 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.041 1.27e-02 6.20e+03 1.03e+01
  ... (remaining 7453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.23: 10335
        6.23 -    12.46: 34
       12.46 -    18.69: 8
       18.69 -    24.92: 3
       24.92 -    31.15: 3
  Bond angle restraints: 10383
  Sorted by residual:
  angle pdb=" N   TYR K  32 "
        pdb=" CA  TYR K  32 "
        pdb=" C   TYR K  32 "
      ideal   model   delta    sigma   weight residual
     109.96   78.81   31.15 1.50e+00 4.44e-01 4.31e+02
  angle pdb=" C   ARG B 529 "
        pdb=" CA  ARG B 529 "
        pdb=" CB  ARG B 529 "
      ideal   model   delta    sigma   weight residual
     110.94   81.56   29.38 1.65e+00 3.67e-01 3.17e+02
  angle pdb=" N   LYS K  33 "
        pdb=" CA  LYS K  33 "
        pdb=" CB  LYS K  33 "
      ideal   model   delta    sigma   weight residual
     110.37   83.48   26.89 1.78e+00 3.16e-01 2.28e+02
  angle pdb=" N   ARG B 529 "
        pdb=" CA  ARG B 529 "
        pdb=" C   ARG B 529 "
      ideal   model   delta    sigma   weight residual
     112.72  128.78  -16.06 1.14e+00 7.69e-01 1.98e+02
  angle pdb=" N   GLU K  43 "
        pdb=" CA  GLU K  43 "
        pdb=" C   GLU K  43 "
      ideal   model   delta    sigma   weight residual
     110.33   93.31   17.02 1.29e+00 6.01e-01 1.74e+02
  ... (remaining 10378 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.86: 4306
       33.86 -    67.71: 277
       67.71 -   101.57: 40
      101.57 -   135.43: 3
      135.43 -   169.28: 3
  Dihedral angle restraints: 4629
    sinusoidal: 2487
      harmonic: 2142
  Sorted by residual:
  dihedral pdb=" C   ARG B 529 "
           pdb=" N   ARG B 529 "
           pdb=" CA  ARG B 529 "
           pdb=" CB  ARG B 529 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -94.98  -27.62     0      2.50e+00 1.60e-01 1.22e+02
  dihedral pdb=" N   LYS K  33 "
           pdb=" C   LYS K  33 "
           pdb=" CA  LYS K  33 "
           pdb=" CB  LYS K  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80   96.34   26.46     0      2.50e+00 1.60e-01 1.12e+02
  dihedral pdb=" C   TYR K  32 "
           pdb=" N   TYR K  32 "
           pdb=" CA  TYR K  32 "
           pdb=" CB  TYR K  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -97.19  -25.41     0      2.50e+00 1.60e-01 1.03e+02
  ... (remaining 4626 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 1181
       0.125 -    0.249: 32
       0.249 -    0.374: 2
       0.374 -    0.499: 14
       0.499 -    0.623: 9
  Chirality restraints: 1238
  Sorted by residual:
  chirality pdb=" CA  TYR K  32 "
            pdb=" N   TYR K  32 "
            pdb=" C   TYR K  32 "
            pdb=" CB  TYR K  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.13   -0.62 2.00e-01 2.50e+01 9.72e+00
  chirality pdb=" P     U T  44 "
            pdb=" OP1   U T  44 "
            pdb=" OP2   U T  44 "
            pdb=" O5'   U T  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.98   -0.57 2.00e-01 2.50e+01 8.16e+00
  chirality pdb=" P     C T  40 "
            pdb=" OP1   C T  40 "
            pdb=" OP2   C T  40 "
            pdb=" O5'   C T  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.98   -0.57 2.00e-01 2.50e+01 8.00e+00
  ... (remaining 1235 not shown)

  Planarity restraints: 1083
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 532 "   -1.008 9.50e-02 1.11e+02   4.52e-01 1.23e+02
        pdb=" NE  ARG B 532 "    0.058 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 532 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 532 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 532 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG K 163 "   -0.809 9.50e-02 1.11e+02   3.63e-01 8.01e+01
        pdb=" NE  ARG K 163 "    0.051 2.00e-02 2.50e+03
        pdb=" CZ  ARG K 163 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG K 163 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG K 163 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 526 "    0.016 2.00e-02 2.50e+03   3.10e-02 9.64e+00
        pdb=" C   ASP B 526 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ASP B 526 "    0.020 2.00e-02 2.50e+03
        pdb=" N   VAL B 527 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1080 not shown)

  Histogram of nonbonded interaction distances:
        0.99 -     1.77: 7
        1.77 -     2.56: 162
        2.56 -     3.34: 10118
        3.34 -     4.12: 19580
        4.12 -     4.90: 32785
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 62652
  Sorted by model distance:
  nonbonded pdb=" CE1 HIS C  73 "
            pdb=" O4'   G T   1 "
     model   vdw
     0.994 3.260
  nonbonded pdb=" CE1 PHE C  21 "
            pdb=" N7    A T  76 "
     model   vdw
     1.188 3.420
  nonbonded pdb=" CZ  PHE C  21 "
            pdb=" C5    A T  76 "
     model   vdw
     1.329 3.560
  nonbonded pdb=" CE1 PHE C  21 "
            pdb=" C5    A T  76 "
     model   vdw
     1.449 3.560
  nonbonded pdb=" CD1 PHE C  21 "
            pdb=" N7    A T  76 "
     model   vdw
     1.565 3.420
  ... (remaining 62647 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=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.540
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4405
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      :  0.005   0.050   7458  Z= 0.350
  Angle     :  1.223  31.151  10383  Z= 0.809
  Chirality :  0.083   0.623   1238
  Planarity :  0.018   0.452   1083
  Dihedral  : 21.010 169.283   3249
  Min Nonbonded Distance : 0.994

Molprobity Statistics.
  All-atom Clashscore : 27.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.43 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.33 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.87 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.31), residues: 731
  helix:  0.13 (0.27), residues: 348
  sheet: -0.51 (0.57), residues: 95
  loop : -1.83 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG K 163 
 TYR   0.019   0.002   TYR K 226 
 PHE   0.011   0.001   PHE B 506 
 TRP   0.027   0.002   TRP P  72 
 HIS   0.002   0.001   HIS K 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00516 /  0.35 ( 7458)
  covalent geometry    : angle       1.22269 /  0.81 (10383)
  hydrogen bonds       : bond        0.15986 / 10.79 (  357)
  hydrogen bonds       : angle       6.88297 /  4.81 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  413 MET cc_start: 0.4362 (mtm) cc_final: 0.3609 (mtm)
REVERT: B  470 LEU cc_start: 0.6469 (mp) cc_final: 0.5907 (tt)
REVERT: C   60 MET cc_start: 0.5579 (tmm) cc_final: 0.4329 (mtm)
REVERT: C   70 ARG cc_start: 0.5801 (mtt-85) cc_final: 0.5425 (tpt170)
REVERT: C  115 ASN cc_start: 0.8670 (p0) cc_final: 0.7844 (p0)
REVERT: C  116 GLU cc_start: 0.8302 (pp20) cc_final: 0.8003 (pm20)
REVERT: K  204 THR cc_start: 0.8004 (m) cc_final: 0.7645 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0936
  time to fit residues: 19.7959
Evaluate side-chains
  99 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    9.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  17 ASN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5167 r_free = 0.5167 target = 0.185475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.162355 restraints weight = 21745.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.166579 restraints weight = 12020.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4943 r_free = 0.4943 target = 0.169202 restraints weight = 7926.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4972 r_free = 0.4972 target = 0.171073 restraints weight = 5923.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4990 r_free = 0.4990 target = 0.172329 restraints weight = 4797.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.4977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4977 r_free = 0.4977    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4976 r_free = 0.4976    target_work(ls_wunit_k1) = 0.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.4976
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4619
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   7458  Z= 0.217
  Angle     :  0.854  10.646  10383  Z= 0.453
  Chirality :  0.052   0.306   1238
  Planarity :  0.008   0.159   1083
  Dihedral  : 23.040 171.442   1841
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 20.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.77 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.27 (0.30), residues: 731
  helix: -0.25 (0.26), residues: 356
  sheet: -0.63 (0.54), residues: 99
  loop : -1.58 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C   9 
 TYR   0.021   0.003   TYR B 510 
 PHE   0.037   0.004   PHE C  21 
 TRP   0.013   0.003   TRP C  59 
 HIS   0.012   0.003   HIS K 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.22 ( 7458)
  covalent geometry    : angle       0.85388 /  0.45 (10383)
  hydrogen bonds       : bond        0.06589 /  4.53 (  357)
  hydrogen bonds       : angle       6.01294 /  4.15 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.5118 (tmm) cc_final: 0.4672 (ptp)
REVERT: C   61 GLU cc_start: 0.5905 (tp30) cc_final: 0.5301 (mt-10)
REVERT: C   70 ARG cc_start: 0.5967 (mtt-85) cc_final: 0.5225 (tpt170)
REVERT: C  117 ASP cc_start: 0.7992 (m-30) cc_final: 0.7592 (m-30)
REVERT: C  121 LEU cc_start: 0.7351 (mm) cc_final: 0.7053 (tp)
  outliers start: 14
  outliers final: 7
  residues processed: 118
  average time/residue: 0.0749
  time to fit residues: 11.5786
Evaluate side-chains
  96 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   86 THR
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 60 optimal weight:    0.0020
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.8990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 417 ASN
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  22 ASN
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5074 r_free = 0.5074 target = 0.179221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.155146 restraints weight = 21586.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4792 r_free = 0.4792 target = 0.159152 restraints weight = 12411.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4830 r_free = 0.4830 target = 0.161903 restraints weight = 8269.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4857 r_free = 0.4857 target = 0.163838 restraints weight = 6129.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.165010 restraints weight = 4913.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.4861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4824
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   7458  Z= 0.184
  Angle     :  0.756  11.231  10383  Z= 0.398
  Chirality :  0.047   0.280   1238
  Planarity :  0.005   0.055   1083
  Dihedral  : 22.851 169.989   1841
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 20.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 17.40 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.30), residues: 731
  helix: -0.20 (0.26), residues: 355
  sheet: -0.76 (0.52), residues: 99
  loop : -1.58 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C   9 
 TYR   0.021   0.003   TYR B 510 
 PHE   0.015   0.002   PHE B 457 
 TRP   0.014   0.002   TRP K 302 
 HIS   0.014   0.003   HIS B 443 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.18 ( 7458)
  covalent geometry    : angle       0.75597 /  0.40 (10383)
  hydrogen bonds       : bond        0.06155 /  4.21 (  357)
  hydrogen bonds       : angle       5.58714 /  3.90 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.5441 (tmm) cc_final: 0.4956 (ptp)
REVERT: C   61 GLU cc_start: 0.6022 (tp30) cc_final: 0.5267 (mt-10)
REVERT: C   70 ARG cc_start: 0.6076 (mtt-85) cc_final: 0.5269 (tpt170)
REVERT: C   72 ILE cc_start: 0.2281 (OUTLIER) cc_final: 0.2024 (mt)
REVERT: C  115 ASN cc_start: 0.8368 (p0) cc_final: 0.7669 (p0)
REVERT: C  124 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6940 (pm20)
REVERT: K    1 MET cc_start: -0.0281 (tpp) cc_final: -0.0639 (tpp)
REVERT: K  204 THR cc_start: 0.7151 (m) cc_final: 0.6762 (p)
  outliers start: 25
  outliers final: 15
  residues processed: 125
  average time/residue: 0.0648
  time to fit residues: 10.8138
Evaluate side-chains
  103 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   72 ILE
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   32 TYR
Chi-restraints excluded: chain K residue   86 THR
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  191 THR
Chi-restraints excluded: chain K residue  304 SER
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 74 optimal weight:   20.0000
   chunk 44 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 51 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 18 optimal weight:    7.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 417 ASN
C  73 HIS
** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5075 r_free = 0.5075 target = 0.178998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.154752 restraints weight = 21705.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4789 r_free = 0.4789 target = 0.158810 restraints weight = 12338.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4828 r_free = 0.4828 target = 0.161567 restraints weight = 8193.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4855 r_free = 0.4855 target = 0.163452 restraints weight = 6075.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4874 r_free = 0.4874 target = 0.164798 restraints weight = 4873.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4898
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7458  Z= 0.166
  Angle     :  0.732  12.455  10383  Z= 0.383
  Chirality :  0.047   0.286   1238
  Planarity :  0.005   0.081   1083
  Dihedral  : 22.721 170.234   1841
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 18.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 19.19 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.29), residues: 731
  helix: -0.05 (0.26), residues: 354
  sheet: -0.63 (0.54), residues: 99
  loop : -1.65 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 377 
 TYR   0.019   0.002   TYR B 510 
 PHE   0.020   0.003   PHE B 394 
 TRP   0.014   0.002   TRP K 291 
 HIS   0.007   0.002   HIS K 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00360 /  0.17 ( 7458)
  covalent geometry    : angle       0.73227 /  0.38 (10383)
  hydrogen bonds       : bond        0.06052 /  4.14 (  357)
  hydrogen bonds       : angle       5.47831 /  3.80 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.5509 (tmm) cc_final: 0.4615 (mtt)
REVERT: C   61 GLU cc_start: 0.6347 (tp30) cc_final: 0.5874 (tt0)
REVERT: C   70 ARG cc_start: 0.6017 (mtt-85) cc_final: 0.5249 (tpt170)
REVERT: C  115 ASN cc_start: 0.8301 (p0) cc_final: 0.7972 (p0)
REVERT: C  117 ASP cc_start: 0.7810 (m-30) cc_final: 0.7131 (m-30)
REVERT: C  119 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7527 (mm-30)
REVERT: C  121 LEU cc_start: 0.7708 (mm) cc_final: 0.7381 (tp)
REVERT: C  124 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6873 (pm20)
REVERT: K    1 MET cc_start: -0.0221 (tpp) cc_final: -0.0481 (tpp)
REVERT: K  204 THR cc_start: 0.7268 (m) cc_final: 0.6923 (p)
  outliers start: 26
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0580
  time to fit residues: 9.9990
Evaluate side-chains
  101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   32 TYR
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  304 SER
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 72 optimal weight:   30.0000
   chunk 45 optimal weight:    0.0370
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 76 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.5858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5079 r_free = 0.5079 target = 0.179275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.154794 restraints weight = 21637.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4791 r_free = 0.4791 target = 0.158959 restraints weight = 12472.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.161815 restraints weight = 8312.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.163759 restraints weight = 6135.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.165057 restraints weight = 4881.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.4863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4942
moved from start:          0.4635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   7458  Z= 0.165
  Angle     :  0.739  13.002  10383  Z= 0.379
  Chirality :  0.048   0.289   1238
  Planarity :  0.004   0.031   1083
  Dihedral  : 22.609 170.176   1841
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 19.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.63 %
    Favored  : 74.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.29), residues: 731
  helix: -0.10 (0.26), residues: 355
  sheet: -0.66 (0.52), residues: 101
  loop : -1.54 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 362 
 TYR   0.017   0.002   TYR B 510 
 PHE   0.022   0.002   PHE B 394 
 TRP   0.028   0.003   TRP P  72 
 HIS   0.006   0.002   HIS C  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 7458)
  covalent geometry    : angle       0.73925 /  0.38 (10383)
  hydrogen bonds       : bond        0.05896 /  4.01 (  357)
  hydrogen bonds       : angle       5.42393 /  3.76 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   60 MET cc_start: 0.4724 (tmm) cc_final: 0.4309 (mtt)
REVERT: C   61 GLU cc_start: 0.6381 (tp30) cc_final: 0.5974 (tt0)
REVERT: C  115 ASN cc_start: 0.8321 (p0) cc_final: 0.8082 (p0)
REVERT: K  204 THR cc_start: 0.7150 (m) cc_final: 0.6843 (p)
REVERT: K  248 MET cc_start: 0.3632 (mmm) cc_final: 0.3327 (mmm)
  outliers start: 23
  outliers final: 15
  residues processed: 116
  average time/residue: 0.0582
  time to fit residues: 9.3931
Evaluate side-chains
  100 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   32 TYR
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  304 SER
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 59 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 417 ASN
B 495 HIS
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 256 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5013 r_free = 0.5013 target = 0.171620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.144499 restraints weight = 20731.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.148333 restraints weight = 12186.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.151054 restraints weight = 8400.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.152885 restraints weight = 6419.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.154209 restraints weight = 5267.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.4748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5419
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7458  Z= 0.241
  Angle     :  0.834  12.416  10383  Z= 0.431
  Chirality :  0.050   0.296   1238
  Planarity :  0.006   0.054   1083
  Dihedral  : 22.521 171.018   1841
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 24.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 23.74 %
    Favored  : 71.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.30), residues: 731
  helix: -0.40 (0.26), residues: 361
  sheet: -1.13 (0.48), residues: 119
  loop : -1.59 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K 258 
 TYR   0.045   0.003   TYR K 190 
 PHE   0.026   0.004   PHE K  73 
 TRP   0.019   0.003   TRP B 503 
 HIS   0.011   0.002   HIS K 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00541 /  0.24 ( 7458)
  covalent geometry    : angle       0.83439 /  0.43 (10383)
  hydrogen bonds       : bond        0.07031 /  4.82 (  357)
  hydrogen bonds       : angle       5.80767 /  4.04 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: B  451 ASP cc_start: 0.7248 (t70) cc_final: 0.6802 (t0)
REVERT: B  452 LEU cc_start: 0.5479 (mt) cc_final: 0.5248 (mt)
REVERT: B  461 LYS cc_start: 0.5092 (tptp) cc_final: 0.4391 (tttp)
REVERT: C   60 MET cc_start: 0.5233 (tmm) cc_final: 0.4475 (mtt)
REVERT: C   61 GLU cc_start: 0.6700 (tp30) cc_final: 0.6298 (tt0)
REVERT: C  115 ASN cc_start: 0.8550 (p0) cc_final: 0.8127 (p0)
REVERT: C  117 ASP cc_start: 0.8118 (m-30) cc_final: 0.7686 (m-30)
REVERT: C  124 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7174 (pm20)
REVERT: K  204 THR cc_start: 0.7437 (m) cc_final: 0.6984 (p)
REVERT: K  257 ASN cc_start: 0.5721 (t0) cc_final: 0.5454 (t0)
REVERT: K  266 MET cc_start: 0.0925 (tmm) cc_final: -0.1325 (ttt)
REVERT: K  289 ILE cc_start: 0.4575 (mt) cc_final: 0.4196 (mt)
  outliers start: 32
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0506
  time to fit residues: 9.0216
Evaluate side-chains
  108 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  417 ASN
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  191 THR
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 417 ASN
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
C  31 ASN
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** 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 = 0.5015 r_free = 0.5015 target = 0.171726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.145131 restraints weight = 20635.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.149184 restraints weight = 12049.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.151981 restraints weight = 8197.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4757 r_free = 0.4757 target = 0.153869 restraints weight = 6197.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.155036 restraints weight = 5041.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.4741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5406
moved from start:          0.6084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7458  Z= 0.187
  Angle     :  0.781  13.548  10383  Z= 0.396
  Chirality :  0.047   0.286   1238
  Planarity :  0.004   0.038   1083
  Dihedral  : 22.392 169.983   1841
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 21.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.02 %
    Favored  : 70.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.30), residues: 731
  helix: -0.36 (0.26), residues: 359
  sheet: -1.16 (0.46), residues: 120
  loop : -1.51 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG K 237 
 TYR   0.023   0.002   TYR K 190 
 PHE   0.045   0.003   PHE K 228 
 TRP   0.019   0.003   TRP K 291 
 HIS   0.006   0.001   HIS K 106 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.19 ( 7458)
  covalent geometry    : angle       0.78131 /  0.40 (10383)
  hydrogen bonds       : bond        0.06374 /  4.37 (  357)
  hydrogen bonds       : angle       5.70147 /  3.95 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  451 ASP cc_start: 0.6992 (t70) cc_final: 0.6729 (t0)
REVERT: B  461 LYS cc_start: 0.5360 (tptp) cc_final: 0.4615 (tttp)
REVERT: C   60 MET cc_start: 0.5051 (tmm) cc_final: 0.4268 (mtt)
REVERT: C   61 GLU cc_start: 0.6677 (tp30) cc_final: 0.6299 (tt0)
REVERT: C  115 ASN cc_start: 0.8580 (p0) cc_final: 0.8007 (p0)
REVERT: C  116 GLU cc_start: 0.8141 (pm20) cc_final: 0.7841 (pm20)
REVERT: C  117 ASP cc_start: 0.8303 (m-30) cc_final: 0.7545 (m-30)
REVERT: C  119 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7447 (mm-30)
REVERT: C  121 LEU cc_start: 0.7689 (mm) cc_final: 0.6953 (tp)
REVERT: K    1 MET cc_start: 0.0191 (tpp) cc_final: -0.0170 (tpt)
REVERT: K  101 ILE cc_start: 0.1702 (OUTLIER) cc_final: -0.0219 (tp)
REVERT: K  129 SER cc_start: 0.8820 (m) cc_final: 0.8568 (t)
REVERT: K  177 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5575 (pt0)
REVERT: K  266 MET cc_start: 0.0834 (tmm) cc_final: -0.1328 (ttt)
REVERT: K  289 ILE cc_start: 0.4086 (mt) cc_final: 0.3625 (mt)
  outliers start: 24
  outliers final: 17
  residues processed: 116
  average time/residue: 0.0549
  time to fit residues: 9.0391
Evaluate side-chains
  102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  101 ILE
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  276 VAL
Chi-restraints excluded: chain K residue  291 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0370
   chunk 49 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0070
   chunk 12 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.4676

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 132 ASN
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5037 r_free = 0.5037 target = 0.173493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.147366 restraints weight = 20819.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.151358 restraints weight = 12261.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.154192 restraints weight = 8340.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.156124 restraints weight = 6278.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4806 r_free = 0.4806 target = 0.157551 restraints weight = 5067.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.4781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5327
moved from start:          0.6303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7458  Z= 0.154
  Angle     :  0.764  14.404  10383  Z= 0.385
  Chirality :  0.046   0.289   1238
  Planarity :  0.004   0.036   1083
  Dihedral  : 22.251 170.846   1841
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 19.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 26.34 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.30), residues: 731
  helix: -0.31 (0.26), residues: 361
  sheet: -0.87 (0.48), residues: 115
  loop : -1.42 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG K 215 
 TYR   0.017   0.002   TYR B 415 
 PHE   0.034   0.002   PHE K 228 
 TRP   0.021   0.002   TRP K 291 
 HIS   0.005   0.001   HIS C  40 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 7458)
  covalent geometry    : angle       0.76406 /  0.39 (10383)
  hydrogen bonds       : bond        0.05865 /  4.03 (  357)
  hydrogen bonds       : angle       5.51488 /  3.81 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  461 LYS cc_start: 0.5248 (tptp) cc_final: 0.4602 (tttp)
REVERT: C   19 GLU cc_start: 0.7139 (pm20) cc_final: 0.6803 (pm20)
REVERT: C   60 MET cc_start: 0.5209 (tmm) cc_final: 0.4255 (mtt)
REVERT: C   61 GLU cc_start: 0.6547 (tp30) cc_final: 0.6188 (tt0)
REVERT: C  115 ASN cc_start: 0.8559 (p0) cc_final: 0.7951 (p0)
REVERT: C  116 GLU cc_start: 0.8160 (pm20) cc_final: 0.7836 (pm20)
REVERT: C  117 ASP cc_start: 0.8173 (m-30) cc_final: 0.7349 (m-30)
REVERT: C  119 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: C  121 LEU cc_start: 0.7663 (mm) cc_final: 0.7209 (tp)
REVERT: K    1 MET cc_start: -0.0217 (tpp) cc_final: -0.0492 (tpt)
REVERT: K  177 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5551 (pt0)
REVERT: K  266 MET cc_start: 0.0787 (tmm) cc_final: -0.1328 (ttt)
REVERT: K  288 MET cc_start: 0.5102 (tmm) cc_final: 0.4843 (ppp)
REVERT: K  303 MET cc_start: 0.4466 (tpt) cc_final: 0.4001 (tpt)
  outliers start: 20
  outliers final: 17
  residues processed: 112
  average time/residue: 0.0558
  time to fit residues: 8.9689
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  108 ILE
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  276 VAL
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 72 optimal weight:   30.0000
   chunk 12 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 59 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
C  85 ASN
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5095 r_free = 0.5095 target = 0.176997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4736 r_free = 0.4736 target = 0.151622 restraints weight = 21348.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4802 r_free = 0.4802 target = 0.155900 restraints weight = 12003.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4843 r_free = 0.4843 target = 0.158690 restraints weight = 8048.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4870 r_free = 0.4870 target = 0.160540 restraints weight = 6057.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.161796 restraints weight = 4934.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5364
moved from start:          0.6669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   7458  Z= 0.172
  Angle     :  0.784  14.157  10383  Z= 0.397
  Chirality :  0.046   0.300   1238
  Planarity :  0.004   0.034   1083
  Dihedral  : 22.163 171.614   1841
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 21.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 27.32 %
    Favored  : 68.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.30), residues: 731
  helix: -0.51 (0.26), residues: 361
  sheet: -1.10 (0.46), residues: 119
  loop : -1.29 (0.40), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K 258 
 TYR   0.019   0.002   TYR K 190 
 PHE   0.026   0.002   PHE K 228 
 TRP   0.020   0.003   TRP B 503 
 HIS   0.004   0.001   HIS B 449 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.17 ( 7458)
  covalent geometry    : angle       0.78368 /  0.40 (10383)
  hydrogen bonds       : bond        0.05943 /  4.07 (  357)
  hydrogen bonds       : angle       5.57230 /  3.85 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  461 LYS cc_start: 0.5091 (tptp) cc_final: 0.4597 (tttp)
REVERT: C   19 GLU cc_start: 0.6764 (pm20) cc_final: 0.6550 (pm20)
REVERT: C   60 MET cc_start: 0.5301 (tmm) cc_final: 0.4325 (mtt)
REVERT: C   61 GLU cc_start: 0.6403 (tp30) cc_final: 0.6063 (tt0)
REVERT: C  115 ASN cc_start: 0.8567 (p0) cc_final: 0.7990 (p0)
REVERT: C  116 GLU cc_start: 0.8059 (pm20) cc_final: 0.7834 (pm20)
REVERT: C  117 ASP cc_start: 0.8025 (m-30) cc_final: 0.7624 (m-30)
REVERT: C  119 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7474 (mm-30)
REVERT: K    1 MET cc_start: 0.0174 (tpp) cc_final: -0.0154 (tpt)
REVERT: K   97 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7420 (tp)
REVERT: K  101 ILE cc_start: 0.1914 (OUTLIER) cc_final: -0.0043 (tp)
REVERT: K  266 MET cc_start: 0.0879 (tmm) cc_final: -0.1285 (ttt)
REVERT: K  288 MET cc_start: 0.5556 (tmm) cc_final: 0.5179 (ppp)
REVERT: P    9 LYS cc_start: 0.6606 (tptp) cc_final: 0.6343 (tptp)
  outliers start: 24
  outliers final: 19
  residues processed: 117
  average time/residue: 0.0536
  time to fit residues: 8.8962
Evaluate side-chains
  112 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue   97 LEU
Chi-restraints excluded: chain K residue  101 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  276 VAL
Chi-restraints excluded: chain K residue  291 TRP
Chi-restraints excluded: chain P residue   62 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 70 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
C  71 GLN
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5063 r_free = 0.5063 target = 0.173569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.147886 restraints weight = 21226.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.151964 restraints weight = 12141.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.154640 restraints weight = 8271.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.156486 restraints weight = 6273.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.157750 restraints weight = 5120.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.4833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.7125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   7458  Z= 0.203
  Angle     :  0.835  13.397  10383  Z= 0.421
  Chirality :  0.047   0.306   1238
  Planarity :  0.005   0.041   1083
  Dihedral  : 22.154 171.730   1841
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 23.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 27.97 %
    Favored  : 67.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.30), residues: 731
  helix: -0.61 (0.26), residues: 358
  sheet: -1.02 (0.47), residues: 116
  loop : -1.38 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C  70 
 TYR   0.024   0.002   TYR K 190 
 PHE   0.046   0.004   PHE K 281 
 TRP   0.050   0.004   TRP K 302 
 HIS   0.007   0.001   HIS B 443 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00461 /  0.20 ( 7458)
  covalent geometry    : angle       0.83455 /  0.42 (10383)
  hydrogen bonds       : bond        0.06320 /  4.34 (  357)
  hydrogen bonds       : angle       5.72393 /  3.96 (  964)

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

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

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1462 Ramachandran restraints generated.
    731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  461 LYS cc_start: 0.5287 (tptp) cc_final: 0.4741 (tttp)
REVERT: C   60 MET cc_start: 0.5085 (tmm) cc_final: 0.4071 (mtt)
REVERT: C   71 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6951 (pp30)
REVERT: C  115 ASN cc_start: 0.8575 (p0) cc_final: 0.7981 (p0)
REVERT: C  117 ASP cc_start: 0.8068 (m-30) cc_final: 0.7616 (m-30)
REVERT: C  119 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7516 (mm-30)
REVERT: C  124 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6603 (pm20)
REVERT: K    1 MET cc_start: 0.0375 (tpp) cc_final: 0.0125 (tpt)
REVERT: K   97 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7448 (tp)
REVERT: K  101 ILE cc_start: 0.2110 (OUTLIER) cc_final: 0.0095 (tp)
REVERT: K  113 ILE cc_start: 0.5135 (tp) cc_final: 0.4924 (tp)
REVERT: K  231 LEU cc_start: 0.7017 (mm) cc_final: 0.6794 (mp)
REVERT: K  266 MET cc_start: 0.1251 (tmm) cc_final: -0.0950 (ttt)
REVERT: K  288 MET cc_start: 0.5477 (tmm) cc_final: 0.4895 (ppp)
REVERT: P    9 LYS cc_start: 0.6563 (tptp) cc_final: 0.6329 (tptp)
  outliers start: 27
  outliers final: 18
  residues processed: 124
  average time/residue: 0.0590
  time to fit residues: 10.4480
Evaluate side-chains
  119 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  404 VAL
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   71 GLN
Chi-restraints excluded: chain C residue   73 HIS
Chi-restraints excluded: chain C residue  122 ILE
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue    4 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue   97 LEU
Chi-restraints excluded: chain K residue  101 ILE
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  149 THR
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  223 LEU
Chi-restraints excluded: chain K residue  276 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 17 optimal weight:    0.1980
   chunk 68 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 495 HIS
C  71 GLN
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5086 r_free = 0.5086 target = 0.175347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.150238 restraints weight = 21328.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.154473 restraints weight = 12023.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.157236 restraints weight = 8076.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.159106 restraints weight = 6089.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.160437 restraints weight = 4944.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5424
moved from start:          0.7351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7458  Z= 0.163
  Angle     :  0.826  14.051  10383  Z= 0.415
  Chirality :  0.048   0.464   1238
  Planarity :  0.005   0.040   1083
  Dihedral  : 22.081 171.925   1841
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 22.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 28.62 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.30), residues: 731
  helix: -0.53 (0.26), residues: 360
  sheet: -1.01 (0.46), residues: 118
  loop : -1.14 (0.40), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 237 
 TYR   0.034   0.002   TYR B 352 
 PHE   0.056   0.003   PHE K 228 
 TRP   0.036   0.004   TRP K 302 
 HIS   0.011   0.001   HIS C  73 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.16 ( 7458)
  covalent geometry    : angle       0.82611 /  0.42 (10383)
  hydrogen bonds       : bond        0.05959 /  4.10 (  357)
  hydrogen bonds       : angle       5.64136 /  3.89 (  964)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1216.47 seconds
wall clock time: 21 minutes 38.31 seconds (1298.31 seconds total)