Starting phenix.real_space_refine
on Sun Jun 15 00:37:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nvu_49856/06_2025/9nvu_49856.cif"
  }
  resolution = 2.71
  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=   0.001 sd=   0.024
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: 8
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     228      5.49       5
     Mg      4      5.21       5
     S      29      5.16       5
     C    5249      2.51       5
     N    1763      2.21       5
     O    2380      1.98       5
     H    7515      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17170
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "N"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 857
          Classifications: {'DNA': 27}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 26}
    Chain: "P"
      Number of atoms: 9878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 9878
          Classifications: {'peptide': 603}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 575}
    Chain: "T"
      Number of atoms: 1243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 1243
          Classifications: {'DNA': 39}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 38}
    Chain: "W"
      Number of atoms: 5186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 5186
          Classifications: {'RNA': 162}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 14, 'rna3p_pur': 72, 'rna3p_pyr': 66}
          Link IDs: {'rna2p': 24, 'rna3p': 137}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 2, ' ZN': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "T"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "W"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6503  SG  CYS P 342      12.880  90.185  64.769  1.00 86.94           S
  ATOM   6943  SG  CYS P 371      17.295  91.098  65.045  1.00 92.50           S
  ATOM   6990  SG  CYS P 374      15.624  88.964  67.223  1.00 92.25           S
  ATOM   3459  SG  CYS P 158      51.532  77.898  32.476  1.00 85.56           S
  ATOM   3508  SG  CYS P 161      54.652  78.362  30.877  1.00 87.50           S
  ATOM   4959  SG  CYS P 245      51.805  80.944  30.511  1.00 85.75           S

  Time building chain proxies: 8.13, per 1000 atoms: 0.47
  Number of scatterers: 17170
  At special positions: 0
  Unit cell: (80.025, 126.225, 137.775, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Zn      2     29.99
     S      29     16.00
     P     228     15.00
     Mg      4     11.99
     O    2380      8.00
     N    1763      7.00
     C    5249      6.00
     H    7515      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.08
  Conformation dependent library (CDL) restraints added in 808.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN P 703 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 374 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 342 "
        pdb="ZN    ZN P 703 " - pdb=" SG  CYS P 371 "
      pdb="  ZN P 704 "
        pdb="ZN    ZN P 704 " - pdb=" ND1 HIS P 248 "
        pdb="ZN    ZN P 704 " - pdb=" SG  CYS P 161 "
        pdb="ZN    ZN P 704 " - pdb=" SG  CYS P 245 "
        pdb="ZN    ZN P 704 " - pdb=" SG  CYS P 158 "
      Number of angles added : 3


  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      41.0% alpha, 13.9% beta
      77 base pairs and 149 stacking pairs defined.
    Time for finding SS restraints: 7.57
  Creating SS restraints...
    Processing helix  chain 'P' and resid 18 through 28
    Processing helix  chain 'P' and resid 86 through 88
      No H-bonds generated for 'chain 'P' and resid 86 through 88'
    Processing helix  chain 'P' and resid 89 through 120
    Processing helix  chain 'P' and resid 171 through 181
      removed outlier: 3.700A  pdb=" N   ILE P 179 " --> pdb=" O   LEU P 175 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 186 through 200
    Processing helix  chain 'P' and resid 201 through 217
    Processing helix  chain 'P' and resid 226 through 233
    Processing helix  chain 'P' and resid 245 through 250
      removed outlier: 3.802A  pdb=" N   ALA P 250 " --> pdb=" O   LYS P 246 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 253 through 257
    Processing helix  chain 'P' and resid 266 through 284
      removed outlier: 3.772A  pdb=" N   PHE P 280 " --> pdb=" O   HIS P 276 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 300 through 305
    Processing helix  chain 'P' and resid 310 through 314
    Processing helix  chain 'P' and resid 326 through 335
    Processing helix  chain 'P' and resid 355 through 359
      removed outlier: 4.024A  pdb=" N   ARG P 359 " --> pdb=" O   ARG P 356 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 363 through 365
      No H-bonds generated for 'chain 'P' and resid 363 through 365'
    Processing helix  chain 'P' and resid 371 through 381
    Processing helix  chain 'P' and resid 381 through 392
      removed outlier: 4.005A  pdb=" N   MET P 391 " --> pdb=" O   SER P 387 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 399 through 420
      removed outlier: 3.548A  pdb=" N   VAL P 404 " --> pdb=" O   GLY P 400 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ILE P 409 " --> pdb=" O   LEU P 405 " (cutoff:3.500A)
      Proline residue:  P 410  - end of helix
    Processing helix  chain 'P' and resid 429 through 439
    Processing helix  chain 'P' and resid 444 through 454
    Processing helix  chain 'P' and resid 511 through 524
    Processing helix  chain 'P' and resid 524 through 533
    Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 6
      removed outlier: 6.160A  pdb=" N   TYR P   4 " --> pdb=" O   ILE P  41 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   LEU P  43 " --> pdb=" O   TYR P   4 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   LEU P   6 " --> pdb=" O   LEU P  43 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   GLN P  42 " --> pdb=" O   ALA P  33 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   ALA P  33 " --> pdb=" O   GLN P  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 424 through 428
      removed outlier: 6.333A  pdb=" N   VAL P  55 " --> pdb=" O   VAL P 289 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLU P 295 " --> pdb=" O   GLN P  59 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY P  79 " --> pdb=" O   ALA P  70 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ARG P  72 " --> pdb=" O   GLU P  77 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLU P  77 " --> pdb=" O   ARG P  72 " (cutoff:3.500A)
      removed outlier: 9.165A  pdb=" N   PHE P 469 " --> pdb=" O   LEU P  78 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ARG P  80 " --> pdb=" O   PHE P 469 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   ILE P 471 " --> pdb=" O   ARG P  80 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   HIS P  82 " --> pdb=" O   ILE P 471 " (cutoff:3.500A)
      removed outlier: 7.940A  pdb=" N   GLN P 473 " --> pdb=" O   HIS P  82 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   ILE P  84 " --> pdb=" O   GLN P 473 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   GLU P 470 " --> pdb=" O   VAL P 602 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 349 through 352
    Processing sheet with id=AA4, first strand: chain 'P' and resid 482 through 485
      removed outlier: 3.554A  pdb=" N   HIS P 484 " --> pdb=" O   TYR P 543 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 495 through 498
      removed outlier: 5.258A  pdb=" N   THR P 496 " --> pdb=" O   LEU P 492 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   LEU P 492 " --> pdb=" O   THR P 496 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'P' and resid 585 through 586
      removed outlier: 3.562A  pdb=" N   GLY P 567 " --> pdb=" O   ARG P 576 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL P 555 " --> pdb=" O   LEU P 593 " (cutoff:3.500A)

    201 hydrogen bonds defined for protein.
    567 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      193 hydrogen bonds
      374 hydrogen bond angles
      0 basepair planarities
      77 basepair parallelities
      149 stacking parallelities
  Total time for adding SS restraints: 6.94

  Time building geometry restraints manager: 5.05 seconds

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

  Histogram of bond lengths:
        0.94 -     1.12: 7501
        1.12 -     1.29: 1030
        1.29 -     1.47: 4825
        1.47 -     1.65: 4423
        1.65 -     1.82: 44
  Bond restraints: 17823
  Sorted by residual:
  bond pdb=" C8    A W -14 "
       pdb=" H8    A W -14 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.68e+01
  bond pdb=" C6   DT N  14 "
       pdb=" H6   DT N  14 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N6    A W  63 "
       pdb=" H61   A W  63 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" CE1 HIS P 352 "
       pdb=" HE1 HIS P 352 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ILE P 471 "
       pdb=" H   ILE P 471 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
  ... (remaining 17818 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 28202
        2.83 -     5.66: 3376
        5.66 -     8.49: 575
        8.49 -    11.32: 24
       11.32 -    14.15: 15
  Bond angle restraints: 32192
  Sorted by residual:
  angle pdb=" O3'   U W  82 "
        pdb=" C3'   U W  82 "
        pdb=" C2'   U W  82 "
      ideal   model   delta    sigma   weight residual
     113.70  125.28  -11.58 1.50e+00 4.44e-01 5.96e+01
  angle pdb=" C4'  DC N  -6 "
        pdb=" C3'  DC N  -6 "
        pdb=" O3'  DC N  -6 "
      ideal   model   delta    sigma   weight residual
     110.00  121.22  -11.22 1.50e+00 4.44e-01 5.59e+01
  angle pdb=" O3'   A W  70 "
        pdb=" C3'   A W  70 "
        pdb=" C2'   A W  70 "
      ideal   model   delta    sigma   weight residual
     109.50  120.19  -10.69 1.50e+00 4.44e-01 5.07e+01
  angle pdb=" C5'   U W   2 "
        pdb=" C4'   U W   2 "
        pdb=" C3'   U W   2 "
      ideal   model   delta    sigma   weight residual
     116.00  105.43   10.57 1.50e+00 4.44e-01 4.97e+01
  angle pdb=" C5'   U W 103 "
        pdb=" C4'   U W 103 "
        pdb=" C3'   U W 103 "
      ideal   model   delta    sigma   weight residual
     116.00  105.83   10.17 1.50e+00 4.44e-01 4.60e+01
  ... (remaining 32187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.27: 7500
       35.27 -    70.53: 749
       70.53 -   105.79: 66
      105.79 -   141.06: 2
      141.06 -   176.32: 8
  Dihedral angle restraints: 8325
    sinusoidal: 6320
      harmonic: 2005
  Sorted by residual:
  dihedral pdb=" O4'   U W 102 "
           pdb=" C1'   U W 102 "
           pdb=" N1    U W 102 "
           pdb=" C2    U W 102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   43.54  156.46     1      1.50e+01 4.44e-03 8.18e+01
  dihedral pdb=" C5'   C W  69 "
           pdb=" C4'   C W  69 "
           pdb=" C3'   C W  69 "
           pdb=" O3'   C W  69 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   87.71   59.29     1      8.00e+00 1.56e-02 7.34e+01
  dihedral pdb=" C4'   C W 116 "
           pdb=" C3'   C W 116 "
           pdb=" C2'   C W 116 "
           pdb=" C1'   C W 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   17.02  -52.02     1      8.00e+00 1.56e-02 5.77e+01
  ... (remaining 8322 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 1488
       0.124 -    0.247: 287
       0.247 -    0.371: 28
       0.371 -    0.494: 5
       0.494 -    0.618: 3
  Chirality restraints: 1811
  Sorted by residual:
  chirality pdb=" C3'   A W  70 "
            pdb=" C4'   A W  70 "
            pdb=" O3'   A W  70 "
            pdb=" C2'   A W  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.13   -0.62 2.00e-01 2.50e+01 9.54e+00
  chirality pdb=" C3'   U W  82 "
            pdb=" C4'   U W  82 "
            pdb=" O3'   U W  82 "
            pdb=" C2'   U W  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.97   -0.51 2.00e-01 2.50e+01 6.40e+00
  chirality pdb=" C3'  DT N  -5 "
            pdb=" C4'  DT N  -5 "
            pdb=" O3'  DT N  -5 "
            pdb=" C2'  DT N  -5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.16   -0.50 2.00e-01 2.50e+01 6.15e+00
  ... (remaining 1808 not shown)

  Planarity restraints: 1825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U W  84 "   -0.401 2.00e-02 2.50e+03   1.52e-01 6.94e+02
        pdb=" N1    U W  84 "    0.053 2.00e-02 2.50e+03
        pdb=" C2    U W  84 "    0.121 2.00e-02 2.50e+03
        pdb=" O2    U W  84 "    0.164 2.00e-02 2.50e+03
        pdb=" N3    U W  84 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    U W  84 "   -0.064 2.00e-02 2.50e+03
        pdb=" O4    U W  84 "   -0.194 2.00e-02 2.50e+03
        pdb=" C5    U W  84 "    0.040 2.00e-02 2.50e+03
        pdb=" C6    U W  84 "    0.104 2.00e-02 2.50e+03
        pdb=" H5    U W  84 "    0.031 2.00e-02 2.50e+03
        pdb=" H3    U W  84 "   -0.004 2.00e-02 2.50e+03
        pdb=" H6    U W  84 "    0.128 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG P 109 "    0.529 9.50e-02 1.11e+02   2.43e-01 6.58e+02
        pdb=" NE  ARG P 109 "    0.186 2.00e-02 2.50e+03
        pdb=" CZ  ARG P 109 "    0.084 2.00e-02 2.50e+03
        pdb=" NH1 ARG P 109 "    0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG P 109 "    0.026 2.00e-02 2.50e+03
        pdb="HH11 ARG P 109 "   -0.263 2.00e-02 2.50e+03
        pdb="HH12 ARG P 109 "    0.032 2.00e-02 2.50e+03
        pdb="HH21 ARG P 109 "   -0.318 2.00e-02 2.50e+03
        pdb="HH22 ARG P 109 "    0.188 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U W 117 "   -0.308 2.00e-02 2.50e+03   1.34e-01 5.36e+02
        pdb=" N1    U W 117 "   -0.042 2.00e-02 2.50e+03
        pdb=" C2    U W 117 "    0.047 2.00e-02 2.50e+03
        pdb=" O2    U W 117 "    0.234 2.00e-02 2.50e+03
        pdb=" N3    U W 117 "   -0.036 2.00e-02 2.50e+03
        pdb=" C4    U W 117 "   -0.074 2.00e-02 2.50e+03
        pdb=" O4    U W 117 "   -0.150 2.00e-02 2.50e+03
        pdb=" C5    U W 117 "    0.029 2.00e-02 2.50e+03
        pdb=" C6    U W 117 "    0.062 2.00e-02 2.50e+03
        pdb=" H5    U W 117 "    0.077 2.00e-02 2.50e+03
        pdb=" H3    U W 117 "    0.017 2.00e-02 2.50e+03
        pdb=" H6    U W 117 "    0.145 2.00e-02 2.50e+03
  ... (remaining 1822 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1034
        2.18 -     2.78: 25911
        2.78 -     3.39: 45024
        3.39 -     3.99: 64035
        3.99 -     4.60: 92293
  Nonbonded interactions: 228297
  Sorted by model distance:
  nonbonded pdb=" HG  SER P 511 "
            pdb=" OD2 ASP P 514 "
     model   vdw
     1.573 2.450
  nonbonded pdb=" OE2 GLU P  77 "
            pdb=" HG1 THR P 466 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" O   THR P 486 "
            pdb=" HG  SER P 540 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HG1 THR P  16 "
            pdb=" OP1   A W 184 "
     model   vdw
     1.600 2.450
  nonbonded pdb=" OP2  DC N  -3 "
            pdb=" HG1 THR P  64 "
     model   vdw
     1.621 2.450
  ... (remaining 228292 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.720
  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:             0.250
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     47.690
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   63.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
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      :  0.017   0.656  10315  Z= 0.853
  Angle     :  1.942  25.756  14971  Z= 1.263
  Chirality :  0.099   0.618   1811
  Planarity :  0.028   0.212   1080
  Dihedral  : 22.138 176.323   5164
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 0.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.57 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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: -0.83 (0.32), residues: 601
  helix: -0.53 (0.31), residues: 221
  sheet: -0.00 (0.65), residues: 57
  loop : -0.56 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.020   TRP P 515 
 HIS   0.028   0.005   HIS P 445 
 PHE   0.068   0.015   PHE P 301 
 TYR   0.158   0.020   TYR P 574 
 ARG   0.021   0.002   ARG P  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15344 (  394)
  hydrogen bonds       : angle       6.34601 (  941)
  metal coordination   : bond        0.39216 (    7)
  metal coordination   : angle      22.48539 (    3)
  covalent geometry    : bond        0.01311 (10308)
  covalent geometry    : angle       1.91642 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    7 ASP cc_start: 0.6484 (t0) cc_final: 0.6246 (t0)
REVERT: P   11 LYS cc_start: 0.7682 (mttt) cc_final: 0.7479 (mptt)
REVERT: P   14 MET cc_start: 0.8214 (mmm) cc_final: 0.8006 (mmm)
REVERT: P   51 ILE cc_start: 0.8047 (mt) cc_final: 0.7811 (mp)
REVERT: P  108 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6367 (mm-30)
REVERT: P  294 VAL cc_start: 0.7721 (t) cc_final: 0.7372 (p)
REVERT: P  338 LYS cc_start: 0.7928 (mttt) cc_final: 0.7598 (mtmm)
REVERT: P  356 ARG cc_start: 0.6904 (mtp180) cc_final: 0.6572 (mtp180)
REVERT: P  366 ASN cc_start: 0.7514 (t0) cc_final: 0.6882 (t0)
REVERT: P  458 LYS cc_start: 0.7611 (mttt) cc_final: 0.7381 (mttt)
REVERT: P  470 GLU cc_start: 0.6701 (mm-30) cc_final: 0.5469 (mm-30)
REVERT: P  510 ASP cc_start: 0.8092 (m-30) cc_final: 0.7846 (m-30)
REVERT: P  517 VAL cc_start: 0.7526 (t) cc_final: 0.7233 (m)
REVERT: P  518 ASP cc_start: 0.7523 (m-30) cc_final: 0.7318 (m-30)
REVERT: P  522 GLU cc_start: 0.7517 (tp30) cc_final: 0.6920 (tp30)
REVERT: P  525 LYS cc_start: 0.7303 (mttt) cc_final: 0.6888 (mtpp)
REVERT: P  529 ASP cc_start: 0.7366 (m-30) cc_final: 0.7049 (m-30)
REVERT: P  541 THR cc_start: 0.7455 (m) cc_final: 0.7075 (p)
REVERT: P  561 LYS cc_start: 0.7809 (mttt) cc_final: 0.7428 (mtpp)
REVERT: P  573 LYS cc_start: 0.7790 (mttt) cc_final: 0.7494 (mttm)
REVERT: P  589 LYS cc_start: 0.8114 (mttt) cc_final: 0.7776 (mtpt)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 3.5030
  time to fit residues: 599.2958
Evaluate side-chains
  135 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
P  53 GLN
P  65 ASN
P 407 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.106133 restraints weight = 32155.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.05
r_work: 0.3164 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10315  Z= 0.216
  Angle     :  0.783   7.572  14971  Z= 0.434
  Chirality :  0.045   0.283   1811
  Planarity :  0.007   0.062   1080
  Dihedral  : 23.984 168.151   3899
  Min Nonbonded Distance : 1.788

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  :  8.70 %
    Favored  : 88.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.00 (0.33), residues: 601
  helix:  0.77 (0.33), residues: 226
  sheet:  0.41 (0.63), residues: 66
  loop : -0.62 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P 430 
 HIS   0.007   0.002   HIS P 445 
 PHE   0.015   0.002   PHE P 263 
 TYR   0.011   0.002   TYR P   4 
 ARG   0.009   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05503 (  394)
  hydrogen bonds       : angle       4.33044 (  941)
  metal coordination   : bond        0.01079 (    7)
  metal coordination   : angle       4.16698 (    3)
  covalent geometry    : bond        0.00448 (10308)
  covalent geometry    : angle       0.78045 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 136
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8468 (t) cc_final: 0.8232 (p)
REVERT: P  310 LYS cc_start: 0.8009 (mptt) cc_final: 0.7669 (mptt)
REVERT: P  356 ARG cc_start: 0.7541 (mtp180) cc_final: 0.7283 (mtp180)
REVERT: P  366 ASN cc_start: 0.7992 (t0) cc_final: 0.7432 (t0)
REVERT: P  470 GLU cc_start: 0.7705 (mm-30) cc_final: 0.6541 (mm-30)
REVERT: P  519 MET cc_start: 0.8482 (mmp) cc_final: 0.7790 (mmp)
REVERT: P  522 GLU cc_start: 0.7761 (tp30) cc_final: 0.7291 (tp30)
REVERT: P  529 ASP cc_start: 0.8094 (m-30) cc_final: 0.7840 (m-30)
REVERT: P  591 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7792 (mmm-85)
  outliers start: 14
  outliers final: 7
  residues processed: 141
  average time/residue: 3.0238
  time to fit residues: 451.7776
Evaluate side-chains
  134 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue  302 MET
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  408 ILE
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 53 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0870
   chunk 46 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
P  53 GLN
P  65 ASN
P 276 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.132735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.102213 restraints weight = 31779.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.09
r_work: 0.3101 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.085  10315  Z= 0.319
  Angle     :  0.742   6.940  14971  Z= 0.415
  Chirality :  0.049   0.295   1811
  Planarity :  0.006   0.068   1080
  Dihedral  : 23.823 165.745   3899
  Min Nonbonded Distance : 1.677

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 12.85 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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: -0.04 (0.33), residues: 601
  helix:  0.93 (0.34), residues: 228
  sheet:  0.39 (0.65), residues: 66
  loop : -0.84 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP P 430 
 HIS   0.013   0.003   HIS P 445 
 PHE   0.014   0.002   PHE P 556 
 TYR   0.020   0.002   TYR P   4 
 ARG   0.008   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05478 (  394)
  hydrogen bonds       : angle       4.17135 (  941)
  metal coordination   : bond        0.01398 (    7)
  metal coordination   : angle       4.02879 (    3)
  covalent geometry    : bond        0.00662 (10308)
  covalent geometry    : angle       0.73954 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 117
  time to evaluate  : 1.183 
Fit side-chains
   revert: symmetry clash
REVERT: P  149 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8283 (mtt180)
REVERT: P  294 VAL cc_start: 0.8470 (t) cc_final: 0.8250 (p)
REVERT: P  356 ARG cc_start: 0.7554 (mtp180) cc_final: 0.7293 (mtp180)
REVERT: P  366 ASN cc_start: 0.8097 (t0) cc_final: 0.7400 (t0)
REVERT: P  525 LYS cc_start: 0.8063 (ttpm) cc_final: 0.7625 (ttpp)
REVERT: P  529 ASP cc_start: 0.8101 (m-30) cc_final: 0.7853 (m-30)
  outliers start: 16
  outliers final: 9
  residues processed: 123
  average time/residue: 3.3153
  time to fit residues: 431.7799
Evaluate side-chains
  123 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   27 LYS
Chi-restraints excluded: chain P residue  149 ARG
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  408 ILE
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  461 GLU
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
P  65 ASN
P 406 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.103495 restraints weight = 31871.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.10
r_work: 0.3141 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059  10315  Z= 0.263
  Angle     :  0.666   7.201  14971  Z= 0.371
  Chirality :  0.044   0.233   1811
  Planarity :  0.006   0.063   1080
  Dihedral  : 23.800 167.516   3899
  Min Nonbonded Distance : 1.701

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.42 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.04 (0.33), residues: 601
  helix:  1.20 (0.34), residues: 228
  sheet:  0.27 (0.65), residues: 66
  loop : -0.93 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 430 
 HIS   0.005   0.002   HIS P 484 
 PHE   0.012   0.002   PHE P 556 
 TYR   0.017   0.002   TYR P   4 
 ARG   0.010   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04893 (  394)
  hydrogen bonds       : angle       3.98226 (  941)
  metal coordination   : bond        0.01692 (    7)
  metal coordination   : angle       3.54374 (    3)
  covalent geometry    : bond        0.00550 (10308)
  covalent geometry    : angle       0.66458 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 116
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8489 (t) cc_final: 0.8236 (p)
REVERT: P  356 ARG cc_start: 0.7619 (mtp180) cc_final: 0.7351 (mtp180)
REVERT: P  366 ASN cc_start: 0.8048 (t0) cc_final: 0.7409 (t0)
REVERT: P  408 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7627 (mp)
REVERT: P  529 ASP cc_start: 0.8071 (m-30) cc_final: 0.7817 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 123
  average time/residue: 3.0251
  time to fit residues: 392.7673
Evaluate side-chains
  127 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  402 THR
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  408 ILE
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  461 GLU
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
P 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.132784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.101852 restraints weight = 32095.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.13
r_work: 0.3090 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.078  10315  Z= 0.334
  Angle     :  0.691   6.671  14971  Z= 0.384
  Chirality :  0.048   0.228   1811
  Planarity :  0.006   0.065   1080
  Dihedral  : 23.820 168.585   3899
  Min Nonbonded Distance : 1.682

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.80 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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: -0.04 (0.33), residues: 601
  helix:  1.28 (0.34), residues: 228
  sheet:  0.10 (0.65), residues: 66
  loop : -1.08 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP P 430 
 HIS   0.007   0.002   HIS P 484 
 PHE   0.014   0.002   PHE P 556 
 TYR   0.020   0.002   TYR P   4 
 ARG   0.008   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05280 (  394)
  hydrogen bonds       : angle       3.98373 (  941)
  metal coordination   : bond        0.01460 (    7)
  metal coordination   : angle       3.17354 (    3)
  covalent geometry    : bond        0.00700 (10308)
  covalent geometry    : angle       0.68959 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8478 (t) cc_final: 0.8205 (p)
REVERT: P  336 ASP cc_start: 0.7567 (m-30) cc_final: 0.7335 (t70)
REVERT: P  356 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7350 (mtp180)
REVERT: P  366 ASN cc_start: 0.8126 (t0) cc_final: 0.7913 (t0)
REVERT: P  408 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7610 (mp)
REVERT: P  525 LYS cc_start: 0.8047 (ttpm) cc_final: 0.7522 (ttmm)
REVERT: P  529 ASP cc_start: 0.8088 (m-30) cc_final: 0.7873 (m-30)
REVERT: P  532 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8004 (mtm-85)
  outliers start: 19
  outliers final: 11
  residues processed: 117
  average time/residue: 2.9490
  time to fit residues: 364.5541
Evaluate side-chains
  122 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  402 THR
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  408 ILE
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  461 GLU
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 22 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
P 152 ASN
P 335 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.104120 restraints weight = 31903.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.08
r_work: 0.3150 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.4031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10315  Z= 0.233
  Angle     :  0.626   6.646  14971  Z= 0.349
  Chirality :  0.042   0.196   1811
  Planarity :  0.005   0.060   1080
  Dihedral  : 23.796 168.710   3899
  Min Nonbonded Distance : 1.713

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 13.80 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.10 (0.34), residues: 601
  helix:  1.49 (0.34), residues: 228
  sheet:  0.15 (0.65), residues: 66
  loop : -1.09 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 484 
 PHE   0.011   0.002   PHE P 556 
 TYR   0.015   0.002   TYR P   4 
 ARG   0.006   0.000   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04640 (  394)
  hydrogen bonds       : angle       3.84016 (  941)
  metal coordination   : bond        0.01606 (    7)
  metal coordination   : angle       2.99814 (    3)
  covalent geometry    : bond        0.00486 (10308)
  covalent geometry    : angle       0.62432 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: P   63 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7980 (ttt180)
REVERT: P  356 ARG cc_start: 0.7619 (mtp180) cc_final: 0.7359 (mtp180)
REVERT: P  529 ASP cc_start: 0.8065 (m-30) cc_final: 0.7832 (m-30)
REVERT: P  532 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8096 (mtm-85)
  outliers start: 19
  outliers final: 10
  residues processed: 122
  average time/residue: 3.0151
  time to fit residues: 389.0084
Evaluate side-chains
  119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  398 LYS
Chi-restraints excluded: chain P residue  402 THR
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  461 GLU
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
P 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.134615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103983 restraints weight = 31730.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.07
r_work: 0.3150 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10315  Z= 0.246
  Angle     :  0.624   6.575  14971  Z= 0.348
  Chirality :  0.042   0.193   1811
  Planarity :  0.005   0.059   1080
  Dihedral  : 23.716 168.999   3899
  Min Nonbonded Distance : 1.712

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 15.12 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.15 (0.34), residues: 601
  helix:  1.56 (0.34), residues: 228
  sheet:  0.20 (0.65), residues: 66
  loop : -1.08 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 484 
 PHE   0.011   0.002   PHE P 556 
 TYR   0.016   0.002   TYR P   4 
 ARG   0.005   0.000   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04635 (  394)
  hydrogen bonds       : angle       3.83296 (  941)
  metal coordination   : bond        0.01629 (    7)
  metal coordination   : angle       2.99715 (    3)
  covalent geometry    : bond        0.00512 (10308)
  covalent geometry    : angle       0.62300 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
REVERT: P   63 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.8002 (ttt180)
REVERT: P  295 GLU cc_start: 0.7935 (tt0) cc_final: 0.6836 (tt0)
REVERT: P  338 LYS cc_start: 0.8275 (mttm) cc_final: 0.7994 (mtmm)
REVERT: P  356 ARG cc_start: 0.7585 (mtp180) cc_final: 0.7323 (mtp180)
REVERT: P  470 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6940 (mm-30)
REVERT: P  532 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8097 (mtm-85)
  outliers start: 20
  outliers final: 11
  residues processed: 121
  average time/residue: 3.1991
  time to fit residues: 407.9640
Evaluate side-chains
  121 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  294 VAL
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  461 GLU
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Chi-restraints excluded: chain P residue  590 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
** P 335 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 = 0.3710 r_free = 0.3710 target = 0.135092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104513 restraints weight = 31548.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.07
r_work: 0.3161 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  10315  Z= 0.230
  Angle     :  0.607   6.366  14971  Z= 0.338
  Chirality :  0.041   0.185   1811
  Planarity :  0.006   0.059   1080
  Dihedral  : 23.603 168.950   3899
  Min Nonbonded Distance : 1.711

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 15.88 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.22 (0.34), residues: 601
  helix:  1.68 (0.35), residues: 228
  sheet:  0.19 (0.65), residues: 66
  loop : -1.09 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 484 
 PHE   0.011   0.002   PHE P 556 
 TYR   0.016   0.002   TYR P   4 
 ARG   0.005   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04517 (  394)
  hydrogen bonds       : angle       3.76539 (  941)
  metal coordination   : bond        0.01687 (    7)
  metal coordination   : angle       2.75820 (    3)
  covalent geometry    : bond        0.00480 (10308)
  covalent geometry    : angle       0.60539 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  336 ASP cc_start: 0.7447 (t70) cc_final: 0.7223 (t0)
REVERT: P  338 LYS cc_start: 0.8263 (mttm) cc_final: 0.7971 (mtmm)
REVERT: P  356 ARG cc_start: 0.7599 (mtp180) cc_final: 0.7338 (mtp180)
REVERT: P  532 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8089 (mtm-85)
  outliers start: 17
  outliers final: 12
  residues processed: 115
  average time/residue: 2.9368
  time to fit residues: 357.2589
Evaluate side-chains
  119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  144 ILE
Chi-restraints excluded: chain P residue  294 VAL
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  426 VAL
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Chi-restraints excluded: chain P residue  590 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 23 optimal weight:    0.0040
   chunk 9 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.8596

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.136124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.105484 restraints weight = 31857.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.07
r_work: 0.3174 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3056 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.4360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10315  Z= 0.194
  Angle     :  0.585   6.269  14971  Z= 0.327
  Chirality :  0.039   0.167   1811
  Planarity :  0.005   0.057   1080
  Dihedral  : 23.510 168.141   3899
  Min Nonbonded Distance : 1.743

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.20 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.36 (0.34), residues: 601
  helix:  1.79 (0.35), residues: 228
  sheet:  0.23 (0.66), residues: 66
  loop : -0.99 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 523 
 PHE   0.010   0.001   PHE P 556 
 TYR   0.013   0.001   TYR P   4 
 ARG   0.005   0.001   ARG P  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  394)
  hydrogen bonds       : angle       3.69654 (  941)
  metal coordination   : bond        0.01842 (    7)
  metal coordination   : angle       3.02566 (    3)
  covalent geometry    : bond        0.00404 (10308)
  covalent geometry    : angle       0.58360 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: P  336 ASP cc_start: 0.7426 (t70) cc_final: 0.7200 (t0)
REVERT: P  338 LYS cc_start: 0.8245 (mttm) cc_final: 0.7996 (mtmm)
REVERT: P  356 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7343 (mtp180)
REVERT: P  532 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8239 (mtm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 112
  average time/residue: 3.1091
  time to fit residues: 367.1687
Evaluate side-chains
  122 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue  294 VAL
Chi-restraints excluded: chain P residue  376 GLU
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  521 LYS
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 24 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
P 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.137103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106592 restraints weight = 31716.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 1.07
r_work: 0.3199 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10315  Z= 0.157
  Angle     :  0.572   6.301  14971  Z= 0.320
  Chirality :  0.038   0.156   1811
  Planarity :  0.005   0.055   1080
  Dihedral  : 23.478 168.210   3899
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.20 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.48 (0.35), residues: 601
  helix:  1.92 (0.35), residues: 228
  sheet:  0.25 (0.67), residues: 66
  loop : -0.93 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P 430 
 HIS   0.007   0.001   HIS P 523 
 PHE   0.008   0.001   PHE P 263 
 TYR   0.013   0.001   TYR P   4 
 ARG   0.007   0.001   ARG P 591 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04107 (  394)
  hydrogen bonds       : angle       3.65288 (  941)
  metal coordination   : bond        0.01863 (    7)
  metal coordination   : angle       3.02863 (    3)
  covalent geometry    : bond        0.00325 (10308)
  covalent geometry    : angle       0.57037 (14968)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
REVERT: P  336 ASP cc_start: 0.7433 (t70) cc_final: 0.7208 (t0)
REVERT: P  338 LYS cc_start: 0.8242 (mttm) cc_final: 0.8001 (mtmm)
REVERT: P  356 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7355 (mtp180)
REVERT: P  532 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8247 (mtm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 120
  average time/residue: 2.9220
  time to fit residues: 370.5046
Evaluate side-chains
  110 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   30 GLN
Chi-restraints excluded: chain P residue  294 VAL
Chi-restraints excluded: chain P residue  403 SER
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  456 HIS
Chi-restraints excluded: chain P residue  521 LYS
Chi-restraints excluded: chain P residue  532 ARG
Chi-restraints excluded: chain P residue  541 THR
Chi-restraints excluded: chain P residue  569 ILE
Chi-restraints excluded: chain P residue  590 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0570
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 21 optimal weight:   30.0000
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
P 406 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.137474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.106959 restraints weight = 31647.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 1.07
r_work: 0.3205 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10315  Z= 0.162
  Angle     :  0.564   6.325  14971  Z= 0.316
  Chirality :  0.037   0.152   1811
  Planarity :  0.005   0.055   1080
  Dihedral  : 23.404 168.192   3899
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.58 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    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:  0.42 (0.35), residues: 601
  helix:  1.84 (0.35), residues: 232
  sheet:  0.23 (0.67), residues: 66
  loop : -0.98 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 523 
 PHE   0.009   0.001   PHE P 301 
 TYR   0.013   0.001   TYR P   4 
 ARG   0.004   0.000   ARG P 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04018 (  394)
  hydrogen bonds       : angle       3.61848 (  941)
  metal coordination   : bond        0.01871 (    7)
  metal coordination   : angle       3.02822 (    3)
  covalent geometry    : bond        0.00337 (10308)
  covalent geometry    : angle       0.56223 (14968)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15853.85 seconds
wall clock time: 272 minutes 24.41 seconds (16344.41 seconds total)