Starting phenix.real_space_refine
on Thu Sep 18 12:27:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nvu_49856/09_2025/9nvu_49856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nvu_49856/09_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_49856/09_2025/9nvu_49856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nvu_49856/09_2025/9nvu_49856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nvu_49856/09_2025/9nvu_49856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nvu_49856/09_2025/9nvu_49856.cif"
  }
  resolution = 2.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.11, per 1000 atoms: 0.18
  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: 1.39
  Conformation dependent library (CDL) restraints added in 361.5 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  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: 3.16
  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: 4.04

  Time building geometry restraints manager: 2.02 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:             1.840
  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:             0.090
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     22.440
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.150
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.021   0.002   ARG P  23 
 TYR   0.158   0.020   TYR P 574 
 PHE   0.068   0.015   PHE P 301 
 TRP   0.041   0.020   TRP P 515 
 HIS   0.028   0.005   HIS P 445 

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

*********************** 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  : 0.334 
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: 0.7007 (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: 1.4411
  time to fit residues: 243.9519
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  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3721 r_free = 0.3721 target = 0.136002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.105587 restraints weight = 32076.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.06
r_work: 0.3166 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3051 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10315  Z= 0.217
  Angle     :  0.783   7.397  14971  Z= 0.437
  Chirality :  0.046   0.291   1811
  Planarity :  0.007   0.065   1080
  Dihedral  : 23.993 169.816   3899
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  :  9.26 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.33), residues: 601
  helix:  0.72 (0.33), residues: 226
  sheet:  0.40 (0.63), residues: 66
  loop : -0.65 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG P  80 
 TYR   0.012   0.002   TYR P   4 
 PHE   0.017   0.002   PHE P 263 
 TRP   0.006   0.001   TRP P 430 
 HIS   0.007   0.002   HIS P 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10308)
  covalent geometry    : angle       0.78107 (14968)
  hydrogen bonds       : bond        0.05666 (  394)
  hydrogen bonds       : angle       4.37890 (  941)
  metal coordination   : bond        0.01456 (    7)
  metal coordination   : angle       4.20077 (    3)

*********************** 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: 13
    poor density    : 137
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8466 (t) cc_final: 0.8217 (p)
REVERT: P  310 LYS cc_start: 0.8024 (mptt) cc_final: 0.7770 (mptt)
REVERT: P  356 ARG cc_start: 0.7519 (mtp180) cc_final: 0.7268 (mtp180)
REVERT: P  366 ASN cc_start: 0.7975 (t0) cc_final: 0.7438 (t0)
REVERT: P  470 GLU cc_start: 0.7670 (mm-30) cc_final: 0.6493 (mm-30)
REVERT: P  519 MET cc_start: 0.8460 (mmp) cc_final: 0.7782 (mmp)
REVERT: P  522 GLU cc_start: 0.7735 (tp30) cc_final: 0.7291 (tp30)
REVERT: P  591 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7803 (mmm-85)
  outliers start: 13
  outliers final: 7
  residues processed: 141
  average time/residue: 1.4221
  time to fit residues: 211.0595
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  : 0.313 
-------------------------------------------------------------------------------
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 26 optimal weight:    7.9990
   chunk 18 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:   20.0000
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3701 r_free = 0.3701 target = 0.134542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.103994 restraints weight = 32097.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 1.08
r_work: 0.3131 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3014 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
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      :  0.005   0.065  10315  Z= 0.253
  Angle     :  0.695   7.179  14971  Z= 0.389
  Chirality :  0.045   0.293   1811
  Planarity :  0.006   0.064   1080
  Dihedral  : 23.806 165.584   3899
  Min Nonbonded Distance : 1.702

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.33), residues: 601
  helix:  1.04 (0.34), residues: 228
  sheet:  0.39 (0.65), residues: 66
  loop : -0.77 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG P  80 
 TYR   0.017   0.002   TYR P   4 
 PHE   0.013   0.002   PHE P 556 
 TRP   0.006   0.001   TRP P 430 
 HIS   0.011   0.002   HIS P 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (10308)
  covalent geometry    : angle       0.69245 (14968)
  hydrogen bonds       : bond        0.04995 (  394)
  hydrogen bonds       : angle       4.11860 (  941)
  metal coordination   : bond        0.01653 (    7)
  metal coordination   : angle       3.93755 (    3)

*********************** 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
  137 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8454 (t) cc_final: 0.8245 (p)
REVERT: P  356 ARG cc_start: 0.7578 (mtp180) cc_final: 0.7315 (mtp180)
REVERT: P  366 ASN cc_start: 0.8055 (t0) cc_final: 0.7365 (t0)
REVERT: P  525 LYS cc_start: 0.7941 (ttpm) cc_final: 0.7643 (ttpm)
  outliers start: 15
  outliers final: 8
  residues processed: 127
  average time/residue: 1.4551
  time to fit residues: 194.5185
Evaluate side-chains
  122 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  115 LEU
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  569 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:   20.0000
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 18 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 = 0.3687 r_free = 0.3687 target = 0.133429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.102534 restraints weight = 32040.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.12
r_work: 0.3113 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.3646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  10315  Z= 0.308
  Angle     :  0.691   7.372  14971  Z= 0.383
  Chirality :  0.047   0.245   1811
  Planarity :  0.006   0.064   1080
  Dihedral  : 23.812 165.945   3899
  Min Nonbonded Distance : 1.691

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 13.04 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.33), residues: 601
  helix:  1.15 (0.34), residues: 228
  sheet:  0.36 (0.65), residues: 66
  loop : -0.97 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG P  80 
 TYR   0.018   0.002   TYR P   4 
 PHE   0.014   0.002   PHE P 263 
 TRP   0.008   0.001   TRP P 430 
 HIS   0.008   0.002   HIS P 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00642 (10308)
  covalent geometry    : angle       0.68896 (14968)
  hydrogen bonds       : bond        0.05112 (  394)
  hydrogen bonds       : angle       3.94231 (  941)
  metal coordination   : bond        0.01651 (    7)
  metal coordination   : angle       3.36516 (    3)

*********************** 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
  134 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8479 (t) cc_final: 0.8231 (p)
REVERT: P  356 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7293 (mtp180)
REVERT: P  408 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7624 (mp)
REVERT: P  525 LYS cc_start: 0.7825 (ttpm) cc_final: 0.7518 (ttmm)
REVERT: P  532 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8345 (mtm-85)
  outliers start: 17
  outliers final: 10
  residues processed: 123
  average time/residue: 1.5108
  time to fit residues: 194.9892
Evaluate side-chains
  126 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue   63 ARG
Chi-restraints excluded: chain P residue  115 LEU
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  569 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 57 optimal weight:    0.3980
   chunk 69 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
P  65 ASN
P 366 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.136950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106466 restraints weight = 31933.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.06
r_work: 0.3195 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3933

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= 0.175
  Angle     :  0.605   7.152  14971  Z= 0.337
  Chirality :  0.039   0.180   1811
  Planarity :  0.005   0.058   1080
  Dihedral  : 23.743 168.046   3899
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.31 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.34), residues: 601
  helix:  1.55 (0.34), residues: 228
  sheet:  0.39 (0.66), residues: 66
  loop : -0.91 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  80 
 TYR   0.012   0.001   TYR P   4 
 PHE   0.009   0.001   PHE P 301 
 TRP   0.005   0.001   TRP P 430 
 HIS   0.004   0.001   HIS P 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10308)
  covalent geometry    : angle       0.60300 (14968)
  hydrogen bonds       : bond        0.04342 (  394)
  hydrogen bonds       : angle       3.76985 (  941)
  metal coordination   : bond        0.01853 (    7)
  metal coordination   : angle       3.53354 (    3)

*********************** 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
  129 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  294 VAL cc_start: 0.8452 (t) cc_final: 0.8174 (p)
REVERT: P  356 ARG cc_start: 0.7566 (mtp180) cc_final: 0.7317 (mtp180)
  outliers start: 11
  outliers final: 8
  residues processed: 122
  average time/residue: 1.4294
  time to fit residues: 184.1391
Evaluate side-chains
  112 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  115 LEU
Chi-restraints excluded: chain P residue  144 ILE
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  461 GLU
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 70 optimal weight:    1.9990
   chunk 22 optimal weight:   20.0000
   chunk 46 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 24 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0020
   overall best weight:    1.2994

-------------------------------------------------------------------------------
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 = 0.3702 r_free = 0.3702 target = 0.134599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.103745 restraints weight = 31640.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.11
r_work: 0.3150 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 3.23 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.4034

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= 0.264
  Angle     :  0.635   6.856  14971  Z= 0.354
  Chirality :  0.043   0.205   1811
  Planarity :  0.005   0.060   1080
  Dihedral  : 23.748 169.090   3899
  Min Nonbonded Distance : 1.707

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.45 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.34), residues: 601
  helix:  1.52 (0.34), residues: 228
  sheet:  0.23 (0.66), residues: 66
  loop : -0.99 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  80 
 TYR   0.017   0.002   TYR P   4 
 PHE   0.012   0.002   PHE P 556 
 TRP   0.007   0.001   TRP P 430 
 HIS   0.006   0.002   HIS P 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 (10308)
  covalent geometry    : angle       0.63331 (14968)
  hydrogen bonds       : bond        0.04722 (  394)
  hydrogen bonds       : angle       3.80084 (  941)
  metal coordination   : bond        0.01707 (    7)
  metal coordination   : angle       3.05322 (    3)

*********************** 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
  117 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.367 
Fit side-chains
REVERT: P  356 ARG cc_start: 0.7587 (mtp180) cc_final: 0.7327 (mtp180)
REVERT: P  532 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8279 (mtm-85)
  outliers start: 12
  outliers final: 6
  residues processed: 108
  average time/residue: 1.4702
  time to fit residues: 166.8225
Evaluate side-chains
  115 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  115 LEU
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  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 40 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 13 optimal weight:    0.0000
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    1.3590

-------------------------------------------------------------------------------
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
P 366 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.134544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.103671 restraints weight = 31629.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 1.10
r_work: 0.3152 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3036 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.3036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  10315  Z= 0.267
  Angle     :  0.635   6.718  14971  Z= 0.352
  Chirality :  0.043   0.203   1811
  Planarity :  0.006   0.058   1080
  Dihedral  : 23.723 168.723   3899
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.26 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.34), residues: 601
  helix:  1.63 (0.34), residues: 228
  sheet:  0.13 (0.65), residues: 66
  loop : -1.06 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG P 475 
 TYR   0.017   0.002   TYR P   4 
 PHE   0.012   0.002   PHE P 556 
 TRP   0.005   0.001   TRP P 430 
 HIS   0.005   0.002   HIS P 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 (10308)
  covalent geometry    : angle       0.63371 (14968)
  hydrogen bonds       : bond        0.04714 (  394)
  hydrogen bonds       : angle       3.78431 (  941)
  metal coordination   : bond        0.01609 (    7)
  metal coordination   : angle       2.90071 (    3)

*********************** 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
  124 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.350 
Fit side-chains
REVERT: P  356 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7384 (mtp180)
REVERT: P  460 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7035 (mm-30)
REVERT: P  461 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7395 (mm-30)
REVERT: P  532 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8305 (mtm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 115
  average time/residue: 1.4190
  time to fit residues: 171.8902
Evaluate side-chains
  113 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  115 LEU
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  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 58 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0670
   chunk 48 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0870
   overall best weight:    0.5696

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.137789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107372 restraints weight = 31774.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.06
r_work: 0.3211 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10315  Z= 0.147
  Angle     :  0.577   6.624  14971  Z= 0.321
  Chirality :  0.037   0.157   1811
  Planarity :  0.005   0.055   1080
  Dihedral  : 23.643 169.875   3899
  Min Nonbonded Distance : 1.773

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.35), residues: 601
  helix:  1.89 (0.35), residues: 228
  sheet:  0.25 (0.67), residues: 66
  loop : -0.92 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P 591 
 TYR   0.012   0.001   TYR P   4 
 PHE   0.009   0.001   PHE P 263 
 TRP   0.005   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 523 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10308)
  covalent geometry    : angle       0.57489 (14968)
  hydrogen bonds       : bond        0.04076 (  394)
  hydrogen bonds       : angle       3.63579 (  941)
  metal coordination   : bond        0.01919 (    7)
  metal coordination   : angle       3.19622 (    3)

*********************** 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
  111 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.297 
Fit side-chains
REVERT: P  356 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7345 (mtp180)
  outliers start: 10
  outliers final: 6
  residues processed: 107
  average time/residue: 1.4515
  time to fit residues: 163.2431
Evaluate side-chains
  111 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  115 LEU
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  525 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
P 366 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 = 0.3711 r_free = 0.3711 target = 0.135217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.104408 restraints weight = 31676.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 1.08
r_work: 0.3159 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3044 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.4328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  10315  Z= 0.240
  Angle     :  0.608   6.443  14971  Z= 0.339
  Chirality :  0.042   0.190   1811
  Planarity :  0.005   0.056   1080
  Dihedral  : 23.536 168.597   3899
  Min Nonbonded Distance : 1.710

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 18.34 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.34), residues: 601
  helix:  1.80 (0.35), residues: 228
  sheet:  0.14 (0.65), residues: 66
  loop : -0.95 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P 591 
 TYR   0.017   0.002   TYR P   4 
 PHE   0.012   0.002   PHE P 556 
 TRP   0.005   0.001   TRP P 430 
 HIS   0.006   0.002   HIS P 484 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (10308)
  covalent geometry    : angle       0.60692 (14968)
  hydrogen bonds       : bond        0.04544 (  394)
  hydrogen bonds       : angle       3.68697 (  941)
  metal coordination   : bond        0.01682 (    7)
  metal coordination   : angle       2.86386 (    3)

*********************** 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
  113 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: P  356 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7367 (mtp180)
  outliers start: 11
  outliers final: 8
  residues processed: 106
  average time/residue: 1.4264
  time to fit residues: 158.9171
Evaluate side-chains
  105 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
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  408 ILE
Chi-restraints excluded: chain P residue  419 LEU
Chi-restraints excluded: chain P residue  525 LYS
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 80 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3724 r_free = 0.3724 target = 0.136187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.105444 restraints weight = 31477.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 1.07
r_work: 0.3181 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.24 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.4363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10315  Z= 0.183
  Angle     :  0.591   6.540  14971  Z= 0.329
  Chirality :  0.038   0.171   1811
  Planarity :  0.005   0.056   1080
  Dihedral  : 23.531 168.502   3899
  Min Nonbonded Distance : 1.735

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.90 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.35), residues: 601
  helix:  1.86 (0.35), residues: 228
  sheet:  0.17 (0.66), residues: 66
  loop : -0.93 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P 591 
 TYR   0.015   0.001   TYR P   4 
 PHE   0.010   0.001   PHE P 556 
 TRP   0.005   0.001   TRP P 430 
 HIS   0.010   0.002   HIS P 523 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10308)
  covalent geometry    : angle       0.58915 (14968)
  hydrogen bonds       : bond        0.04314 (  394)
  hydrogen bonds       : angle       3.64398 (  941)
  metal coordination   : bond        0.01759 (    7)
  metal coordination   : angle       2.99486 (    3)

********************** 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
  109 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.349 
Fit side-chains
REVERT: P  356 ARG cc_start: 0.7612 (mtp180) cc_final: 0.7366 (mtp180)
REVERT: P  408 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7590 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 104
  average time/residue: 1.4587
  time to fit residues: 159.4824
Evaluate side-chains
  110 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 103
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   17 CYS
Chi-restraints excluded: chain P residue  294 VAL
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  525 LYS
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 39 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
P 366 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 = 0.3734 r_free = 0.3734 target = 0.136873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106258 restraints weight = 31743.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.08
r_work: 0.3191 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.4452

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= 0.185
  Angle     :  0.581   6.212  14971  Z= 0.323
  Chirality :  0.039   0.163   1811
  Planarity :  0.005   0.056   1080
  Dihedral  : 23.488 168.703   3899
  Min Nonbonded Distance : 1.737

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 19.47 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.35), residues: 601
  helix:  1.90 (0.35), residues: 228
  sheet:  0.22 (0.66), residues: 66
  loop : -0.86 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P  80 
 TYR   0.013   0.001   TYR P   4 
 PHE   0.009   0.001   PHE P 556 
 TRP   0.004   0.001   TRP P 430 
 HIS   0.005   0.001   HIS P 523 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10308)
  covalent geometry    : angle       0.57973 (14968)
  hydrogen bonds       : bond        0.04177 (  394)
  hydrogen bonds       : angle       3.60477 (  941)
  metal coordination   : bond        0.01882 (    7)
  metal coordination   : angle       2.99373 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6997.75 seconds
wall clock time: 118 minutes 47.28 seconds (7127.28 seconds total)