Starting phenix.real_space_refine
on Tue Jan 14 19:19:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d85_46630/01_2025/9d85_46630_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d85_46630/01_2025/9d85_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_46630/01_2025/9d85_46630.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d85_46630/01_2025/9d85_46630.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d85_46630/01_2025/9d85_46630_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d85_46630/01_2025/9d85_46630_neut.cif"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.045
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1}
          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: 4.44, per 1000 atoms: 0.62
  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: 2.04
  Conformation dependent library (CDL) restraints added in 882.5 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: 2.56
  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: 2.51

  Time building geometry restraints manager: 2.31 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=" 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
  bond pdb=" C   LYS K  33 "
       pdb=" N   PRO K  34 "
    ideal  model  delta    sigma   weight residual
    1.329  1.365 -0.036 1.18e-02 7.18e+03 9.17e+00
  bond pdb=" N   LYS K  33 "
       pdb=" CA  LYS K  33 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.042 1.41e-02 5.03e+03 8.70e+00
  bond pdb=" O5'   U T  44 "
       pdb=" C5'   U T  44 "
    ideal  model  delta    sigma   weight residual
    1.420  1.464 -0.044 1.50e-02 4.44e+03 8.63e+00
  ... (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: 1168
       0.125 -    0.249: 45
       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:             1.520
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.570
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4417
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= 0.321
  Angle     :  1.213  31.151  10383  Z= 0.765
  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 : 27.16
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.027   0.002   TRP P  72 
 HIS   0.002   0.001   HIS K 106 
 PHE   0.011   0.001   PHE B 506 
 TYR   0.019   0.002   TYR K 226 
 ARG   0.007   0.001   ARG K 163 

*********************** 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  : 0.717 
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: 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: 0.6470 (mp) cc_final: 0.5907 (tt)
REVERT: C   60 MET cc_start: 0.5579 (tmm) cc_final: 0.4348 (mtt)
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: 0.8457 (p0)
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: 0.2559
  time to fit residues: 52.9745
Evaluate side-chains
  101 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.3980
   chunk 59 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0670
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:   10.0000
   overall best weight:    1.0722

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

Flipped N/Q/H residues before XYZ refinement:
** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  17 ASN
C  22 ASN
** C  28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  73 HIS
K 160 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5067 r_free = 0.5067 target = 0.178071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.153521 restraints weight = 21133.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.157523 restraints weight = 12050.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.160312 restraints weight = 8100.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.4788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4788 r_free = 0.4788    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4787 r_free = 0.4787    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.4787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5074
moved from start:          0.4030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7458  Z= 0.268
  Angle     :  0.807   7.730  10383  Z= 0.420
  Chirality :  0.048   0.201   1238
  Planarity :  0.006   0.082   1083
  Dihedral  : 22.986 168.451   1841
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 19.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.63 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.30), residues: 731
  helix:  0.09 (0.26), residues: 352
  sheet: -0.87 (0.52), residues: 99
  loop : -1.48 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP K 291 
 HIS   0.009   0.003   HIS K 106 
 PHE   0.028   0.003   PHE B 457 
 TYR   0.022   0.003   TYR B 510 
 ARG   0.005   0.001   ARG B 368 

*********************** 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
  141 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.668 
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  451 ASP cc_start: 0.6594 (t70) cc_final: 0.6379 (t0)
REVERT: B  461 LYS cc_start: 0.4686 (tptp) cc_final: 0.4019 (tptp)
REVERT: B  470 LEU cc_start: 0.6436 (mp) cc_final: 0.5996 (tt)
REVERT: B  473 ILE cc_start: 0.6657 (OUTLIER) cc_final: 0.6351 (mm)
REVERT: C  115 ASN cc_start: 0.8646 (p0) cc_final: 0.8117 (p0)
REVERT: C  124 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7282 (pm20)
REVERT: K    1 MET cc_start: 0.0071 (mmm) cc_final: -0.0580 (tpp)
  outliers start: 16
  outliers final: 8
  residues processed: 129
  average time/residue: 0.2259
  time to fit residues: 37.9007
Evaluate side-chains
  102 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
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  473 ILE
Chi-restraints excluded: chain B residue  492 LEU
Chi-restraints excluded: chain C residue   20 ILE
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  124 GLU
Chi-restraints excluded: chain C residue  147 LEU
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue  108 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 52 optimal weight:    0.2980
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9980
   chunk 59 optimal weight:    0.2980
   chunk 18 optimal weight:    0.0030
   chunk 5 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
B 417 ASN
K 132 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5152 r_free = 0.5152 target = 0.183078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.158854 restraints weight = 21909.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.163309 restraints weight = 11783.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.166280 restraints weight = 7716.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.4903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5077
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7458  Z= 0.213
  Angle     :  0.702  10.917  10383  Z= 0.357
  Chirality :  0.043   0.175   1238
  Planarity :  0.004   0.035   1083
  Dihedral  : 22.579 167.046   1841
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 18.70 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.30), residues: 731
  helix:  0.22 (0.27), residues: 355
  sheet: -0.78 (0.53), residues: 99
  loop : -1.44 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP K 291 
 HIS   0.005   0.001   HIS K 106 
 PHE   0.019   0.002   PHE C  21 
 TYR   0.014   0.002   TYR B 400 
 ARG   0.004   0.001   ARG K  84 

*********************** 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
  139 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 115
  time to evaluate  : 0.724 
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: B  442 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4567 (tt)
REVERT: B  461 LYS cc_start: 0.4448 (tptp) cc_final: 0.4101 (tptm)
REVERT: B  470 LEU cc_start: 0.6273 (mp) cc_final: 0.5829 (tt)
REVERT: C  115 ASN cc_start: 0.8386 (p0) cc_final: 0.7909 (p0)
REVERT: K   -2 MET cc_start: 0.2597 (tpt) cc_final: 0.1823 (tpt)
REVERT: K    1 MET cc_start: -0.0281 (mmm) cc_final: -0.1013 (tpp)
REVERT: K  164 TYR cc_start: 0.4536 (m-10) cc_final: 0.4177 (m-10)
REVERT: K  204 THR cc_start: 0.7217 (m) cc_final: 0.6854 (p)
REVERT: K  289 ILE cc_start: 0.3342 (mt) cc_final: 0.2498 (mt)
REVERT: K  298 LYS cc_start: 0.5085 (tttt) cc_final: 0.4620 (tttt)
  outliers start: 24
  outliers final: 11
  residues processed: 131
  average time/residue: 0.2083
  time to fit residues: 36.1732
Evaluate side-chains
  106 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 ASP
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   85 VAL
Chi-restraints excluded: chain K residue  107 CYS
Chi-restraints excluded: chain K residue  108 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   chunk 67 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.5102 r_free = 0.5102 target = 0.178448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.152820 restraints weight = 21761.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.157353 restraints weight = 11852.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4851 r_free = 0.4851 target = 0.160161 restraints weight = 7914.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.4832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5414
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7458  Z= 0.257
  Angle     :  0.746  15.834  10383  Z= 0.377
  Chirality :  0.044   0.182   1238
  Planarity :  0.005   0.047   1083
  Dihedral  : 22.214 167.039   1841
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 19.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 20.65 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 731
  helix:  0.20 (0.27), residues: 354
  sheet: -0.91 (0.54), residues: 94
  loop : -1.43 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP K 291 
 HIS   0.012   0.002   HIS K 106 
 PHE   0.023   0.003   PHE P  14 
 TYR   0.022   0.002   TYR K 190 
 ARG   0.020   0.001   ARG K  84 

*********************** 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
  143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 115
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  413 MET cc_start: 0.4257 (OUTLIER) cc_final: 0.3717 (ptm)
REVERT: B  442 LEU cc_start: 0.5032 (OUTLIER) cc_final: 0.4656 (tt)
REVERT: B  461 LYS cc_start: 0.5030 (tptp) cc_final: 0.4711 (tptm)
REVERT: C  115 ASN cc_start: 0.8673 (p0) cc_final: 0.8413 (p0)
REVERT: C  124 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7133 (pm20)
REVERT: K   -2 MET cc_start: 0.2878 (tpt) cc_final: 0.2282 (tpt)
REVERT: K   97 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7259 (tp)
REVERT: K  266 MET cc_start: 0.0990 (tmm) cc_final: -0.1096 (ttt)
REVERT: K  289 ILE cc_start: 0.3776 (mt) cc_final: 0.3482 (mt)
REVERT: K  298 LYS cc_start: 0.5424 (tttt) cc_final: 0.4955 (tttt)
  outliers start: 28
  outliers final: 14
  residues processed: 136
  average time/residue: 0.2146
  time to fit residues: 39.3027
Evaluate side-chains
  118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  442 LEU
Chi-restraints excluded: chain B residue  447 VAL
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   20 SER
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   97 LEU
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  107 CYS
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  154 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0370
   chunk 42 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 70 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0670
   chunk 13 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
B 495 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5109 r_free = 0.5109 target = 0.179230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4762 r_free = 0.4762 target = 0.154239 restraints weight = 21391.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.158729 restraints weight = 11898.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4865 r_free = 0.4865 target = 0.161554 restraints weight = 8030.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5434
moved from start:          0.6971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7458  Z= 0.212
  Angle     :  0.704  11.456  10383  Z= 0.354
  Chirality :  0.043   0.180   1238
  Planarity :  0.004   0.040   1083
  Dihedral  : 22.058 169.132   1841
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 25.69 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.30), residues: 731
  helix:  0.31 (0.27), residues: 352
  sheet: -0.71 (0.50), residues: 106
  loop : -1.38 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.003   TRP K 291 
 HIS   0.009   0.002   HIS K 106 
 PHE   0.035   0.002   PHE K 228 
 TYR   0.015   0.002   TYR K 190 
 ARG   0.006   0.000   ARG B 377 

*********************** 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
  130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  442 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4705 (tt)
REVERT: C  115 ASN cc_start: 0.8668 (p0) cc_final: 0.8131 (p0)
REVERT: C  119 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7367 (mm-30)
REVERT: C  124 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7003 (pm20)
REVERT: K    1 MET cc_start: 0.0062 (tpp) cc_final: -0.0676 (tpp)
REVERT: K   97 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7237 (tp)
REVERT: K  266 MET cc_start: 0.1058 (tmm) cc_final: -0.0896 (ttt)
REVERT: K  298 LYS cc_start: 0.5637 (tttt) cc_final: 0.5118 (tttt)
  outliers start: 23
  outliers final: 12
  residues processed: 122
  average time/residue: 0.2008
  time to fit residues: 33.3497
Evaluate side-chains
  105 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
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   20 SER
Chi-restraints excluded: chain K residue   26 PHE
Chi-restraints excluded: chain K residue   97 LEU
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  259 LEU
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 34 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5087 r_free = 0.5087 target = 0.176888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4733 r_free = 0.4733 target = 0.151535 restraints weight = 21276.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4794 r_free = 0.4794 target = 0.155826 restraints weight = 11964.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.158627 restraints weight = 8124.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.4826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5528
moved from start:          0.7731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   7458  Z= 0.221
  Angle     :  0.709  12.183  10383  Z= 0.354
  Chirality :  0.043   0.253   1238
  Planarity :  0.004   0.032   1083
  Dihedral  : 21.894 169.238   1841
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.51 %
    Favored  : 95.49 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 28.46 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.30), residues: 731
  helix:  0.08 (0.26), residues: 358
  sheet: -0.87 (0.48), residues: 114
  loop : -1.40 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP K 291 
 HIS   0.006   0.002   HIS B 495 
 PHE   0.012   0.002   PHE P  43 
 TYR   0.032   0.002   TYR K 314 
 ARG   0.006   0.001   ARG K  84 

*********************** 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
  125 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  442 LEU cc_start: 0.5001 (OUTLIER) cc_final: 0.4734 (tt)
REVERT: C   77 LYS cc_start: 0.6940 (ptpp) cc_final: 0.6659 (pttm)
REVERT: C  115 ASN cc_start: 0.8688 (p0) cc_final: 0.8288 (p0)
REVERT: C  119 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7489 (mm-30)
REVERT: C  124 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6960 (pm20)
REVERT: K    1 MET cc_start: 0.0457 (tpp) cc_final: 0.0009 (tpp)
REVERT: K   97 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7166 (tp)
REVERT: K  266 MET cc_start: 0.1295 (tmm) cc_final: -0.0552 (ttt)
REVERT: K  298 LYS cc_start: 0.6117 (tttt) cc_final: 0.5715 (tttt)
  outliers start: 21
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1669
  time to fit residues: 27.5440
Evaluate side-chains
  109 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  442 LEU
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue  117 ASP
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   97 LEU
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  107 CYS
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  259 LEU
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.169786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.142471 restraints weight = 20881.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.146380 restraints weight = 12221.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4722 r_free = 0.4722 target = 0.149118 restraints weight = 8547.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5847
moved from start:          0.9099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   7458  Z= 0.302
  Angle     :  0.790  13.467  10383  Z= 0.400
  Chirality :  0.044   0.240   1238
  Planarity :  0.005   0.040   1083
  Dihedral  : 21.953 169.848   1841
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 23.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.15 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.30), residues: 731
  helix: -0.14 (0.27), residues: 346
  sheet: -0.82 (0.49), residues: 111
  loop : -1.56 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP K 291 
 HIS   0.013   0.002   HIS K 110 
 PHE   0.041   0.003   PHE K 228 
 TYR   0.032   0.002   TYR B 415 
 ARG   0.006   0.001   ARG K 260 

*********************** 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
  143 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  413 MET cc_start: 0.4663 (OUTLIER) cc_final: 0.4321 (ptt)
REVERT: B  495 HIS cc_start: 0.4974 (m170) cc_final: 0.4659 (m170)
REVERT: C   77 LYS cc_start: 0.7247 (ptpp) cc_final: 0.6988 (ptpp)
REVERT: C  115 ASN cc_start: 0.8702 (p0) cc_final: 0.8256 (p0)
REVERT: C  119 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7232 (mm-30)
REVERT: C  123 ARG cc_start: 0.7037 (mtp85) cc_final: 0.4951 (mmp-170)
REVERT: C  124 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.7078 (pm20)
REVERT: K   97 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7335 (tp)
REVERT: K  266 MET cc_start: 0.2123 (tmm) cc_final: 0.1026 (ttt)
REVERT: K  281 PHE cc_start: 0.5884 (m-80) cc_final: 0.5558 (t80)
REVERT: K  288 MET cc_start: 0.5283 (tmm) cc_final: 0.3694 (ppp)
REVERT: K  298 LYS cc_start: 0.6501 (tttt) cc_final: 0.6190 (tptm)
  outliers start: 29
  outliers final: 17
  residues processed: 135
  average time/residue: 0.1928
  time to fit residues: 35.1333
Evaluate side-chains
  118 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  355 PHE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 ASP
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
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   31 MET
Chi-restraints excluded: chain K residue   97 LEU
Chi-restraints excluded: chain K residue  104 VAL
Chi-restraints excluded: chain K residue  135 VAL
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  178 LEU
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  223 LEU
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    0.5980
   chunk 76 optimal weight:    9.9990
   chunk 52 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 57 optimal weight:    0.3980
   chunk 19 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C  28 GLN
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 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 = 0.5028 r_free = 0.5028 target = 0.169888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.142094 restraints weight = 21006.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4704 r_free = 0.4704 target = 0.146467 restraints weight = 11843.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.149422 restraints weight = 8108.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5776
moved from start:          0.9448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7458  Z= 0.223
  Angle     :  0.732  13.628  10383  Z= 0.369
  Chirality :  0.044   0.242   1238
  Planarity :  0.004   0.036   1083
  Dihedral  : 21.840 169.677   1841
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 19.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 29.43 %
    Favored  : 67.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.30), residues: 731
  helix: -0.06 (0.27), residues: 355
  sheet: -0.66 (0.49), residues: 109
  loop : -1.55 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP K 291 
 HIS   0.004   0.001   HIS B 495 
 PHE   0.012   0.002   PHE K 161 
 TYR   0.020   0.002   TYR B 387 
 ARG   0.005   0.001   ARG B 516 

*********************** 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
  121 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  413 MET cc_start: 0.5061 (mtm) cc_final: 0.4237 (ptp)
REVERT: C    9 ARG cc_start: 0.7294 (mmp80) cc_final: 0.6971 (mmp80)
REVERT: C   27 PHE cc_start: 0.7145 (p90) cc_final: 0.6871 (p90)
REVERT: C   77 LYS cc_start: 0.7276 (ptpp) cc_final: 0.7064 (ptpp)
REVERT: C   78 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8112 (tp)
REVERT: C  115 ASN cc_start: 0.8695 (p0) cc_final: 0.8253 (p0)
REVERT: C  119 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7397 (mm-30)
REVERT: C  123 ARG cc_start: 0.6981 (mtp85) cc_final: 0.5415 (mpt180)
REVERT: C  124 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7076 (pm20)
REVERT: C  138 VAL cc_start: 0.7174 (t) cc_final: 0.6943 (p)
REVERT: K    1 MET cc_start: 0.1392 (tpp) cc_final: 0.0826 (tpp)
REVERT: K  248 MET cc_start: 0.4820 (tpp) cc_final: 0.4276 (tpp)
REVERT: K  266 MET cc_start: 0.2151 (tmm) cc_final: 0.1159 (ttt)
REVERT: K  288 MET cc_start: 0.5060 (OUTLIER) cc_final: 0.4711 (ppp)
REVERT: K  298 LYS cc_start: 0.6658 (tttt) cc_final: 0.6399 (tptm)
  outliers start: 20
  outliers final: 13
  residues processed: 116
  average time/residue: 0.1812
  time to fit residues: 28.8535
Evaluate side-chains
  107 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   78 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   20 SER
Chi-restraints excluded: chain K residue  106 HIS
Chi-restraints excluded: chain K residue  178 LEU
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  223 LEU
Chi-restraints excluded: chain K residue  288 MET
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0770
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.4980
   chunk 42 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** B 495 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5050 r_free = 0.5050 target = 0.170777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4679 r_free = 0.4679 target = 0.144006 restraints weight = 21183.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.148156 restraints weight = 12204.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4782 r_free = 0.4782 target = 0.150995 restraints weight = 8393.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5723
moved from start:          0.9838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7458  Z= 0.201
  Angle     :  0.698  13.360  10383  Z= 0.352
  Chirality :  0.043   0.248   1238
  Planarity :  0.004   0.042   1083
  Dihedral  : 21.697 169.908   1841
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 30.08 %
    Favored  : 66.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.30), residues: 731
  helix:  0.02 (0.27), residues: 356
  sheet: -0.61 (0.49), residues: 109
  loop : -1.60 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP K 291 
 HIS   0.005   0.001   HIS B 495 
 PHE   0.019   0.002   PHE K 228 
 TYR   0.019   0.002   TYR B 387 
 ARG   0.006   0.000   ARG B 516 

*********************** 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
  130 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.708 
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: B  413 MET cc_start: 0.5089 (mtm) cc_final: 0.4301 (ptp)
REVERT: C    9 ARG cc_start: 0.7242 (mmp80) cc_final: 0.6947 (mmp80)
REVERT: C   27 PHE cc_start: 0.7194 (p90) cc_final: 0.6891 (p90)
REVERT: C   77 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6954 (ptpp)
REVERT: C   78 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (tp)
REVERT: C  115 ASN cc_start: 0.8691 (p0) cc_final: 0.8286 (p0)
REVERT: C  119 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7460 (mm-30)
REVERT: C  123 ARG cc_start: 0.7113 (mtp85) cc_final: 0.5612 (mpt180)
REVERT: C  124 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7074 (pm20)
REVERT: C  138 VAL cc_start: 0.7065 (t) cc_final: 0.6823 (p)
REVERT: K    1 MET cc_start: 0.1377 (tpp) cc_final: 0.0927 (tpp)
REVERT: K  248 MET cc_start: 0.4676 (tpp) cc_final: 0.4403 (tpp)
REVERT: K  266 MET cc_start: 0.2025 (tmm) cc_final: 0.1073 (ttt)
REVERT: K  298 LYS cc_start: 0.6776 (tttt) cc_final: 0.6575 (tptm)
  outliers start: 21
  outliers final: 16
  residues processed: 123
  average time/residue: 0.1846
  time to fit residues: 31.1422
Evaluate side-chains
  116 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  422 LYS
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   77 LYS
Chi-restraints excluded: chain C residue   78 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   20 SER
Chi-restraints excluded: chain K residue   85 VAL
Chi-restraints excluded: chain K residue  152 ILE
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  178 LEU
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  223 LEU
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 54 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 74 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 60 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 445 ASN
B 495 HIS
** C  43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 ASN
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 224 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 = 0.4883 r_free = 0.4883 target = 0.156240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.126532 restraints weight = 20804.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.130434 restraints weight = 12121.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.132920 restraints weight = 8540.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6237
moved from start:          1.1374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.098   7458  Z= 0.464
  Angle     :  0.961  15.256  10383  Z= 0.494
  Chirality :  0.052   0.291   1238
  Planarity :  0.007   0.056   1083
  Dihedral  : 22.339 169.338   1841
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 32.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 31.71 %
    Favored  : 64.88 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.14 (0.29), residues: 731
  helix: -0.96 (0.25), residues: 350
  sheet: -1.19 (0.46), residues: 113
  loop : -1.95 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.005   TRP K 291 
 HIS   0.014   0.003   HIS C  43 
 PHE   0.094   0.005   PHE K 228 
 TYR   0.041   0.003   TYR K 190 
 ARG   0.013   0.001   ARG B 377 

********************** 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
  122 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  413 MET cc_start: 0.5238 (mtm) cc_final: 0.4990 (ptm)
REVERT: C   78 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8330 (tp)
REVERT: C  124 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7293 (pm20)
REVERT: C  138 VAL cc_start: 0.7241 (t) cc_final: 0.6882 (p)
REVERT: K    1 MET cc_start: 0.3938 (tpp) cc_final: 0.2938 (tpt)
REVERT: K  298 LYS cc_start: 0.7700 (tttt) cc_final: 0.7307 (tptt)
REVERT: P   55 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7681 (mmmt)
  outliers start: 21
  outliers final: 17
  residues processed: 116
  average time/residue: 0.1846
  time to fit residues: 29.1970
Evaluate side-chains
  111 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  447 VAL
Chi-restraints excluded: chain B residue  448 ILE
Chi-restraints excluded: chain C residue   17 ASN
Chi-restraints excluded: chain C residue   78 ILE
Chi-restraints excluded: chain C residue   96 PHE
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   20 SER
Chi-restraints excluded: chain K residue   31 MET
Chi-restraints excluded: chain K residue  145 VAL
Chi-restraints excluded: chain K residue  152 ILE
Chi-restraints excluded: chain K residue  154 VAL
Chi-restraints excluded: chain K residue  178 LEU
Chi-restraints excluded: chain K residue  186 VAL
Chi-restraints excluded: chain K residue  303 MET
Chi-restraints excluded: chain K residue  311 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 40 optimal weight:    0.7980
   chunk 21 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** K 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4991 r_free = 0.4991 target = 0.164871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4604 r_free = 0.4604 target = 0.138706 restraints weight = 21450.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.142811 restraints weight = 11908.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4705 r_free = 0.4705 target = 0.145479 restraints weight = 8108.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.4693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5967
moved from start:          1.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7458  Z= 0.238
  Angle     :  0.774  12.486  10383  Z= 0.394
  Chirality :  0.046   0.265   1238
  Planarity :  0.005   0.045   1083
  Dihedral  : 22.049 170.793   1841
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 32.85 %
    Favored  : 64.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.30), residues: 731
  helix: -0.42 (0.26), residues: 354
  sheet: -0.85 (0.47), residues: 114
  loop : -1.90 (0.36), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.005   TRP K 291 
 HIS   0.008   0.002   HIS K 110 
 PHE   0.051   0.003   PHE K 228 
 TYR   0.025   0.002   TYR B 387 
 ARG   0.005   0.001   ARG B 516 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2806.82 seconds
wall clock time: 53 minutes 45.85 seconds (3225.85 seconds total)