Starting phenix.real_space_refine
on Thu Aug  6 13:21:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ces_45517/08_2026/9ces_45517_neut.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.036
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: 6
    Type Number    sf(0)   Gaussians
     P     181      5.49       5
     S      38      5.16       5
     C    4897      2.51       5
     N    1619      2.21       5
     O    2103      1.98       5
     H    7001      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 15839
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "N"
      Number of atoms: 475
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 475
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "P"
      Number of atoms: 10029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 10029
          Classifications: {'peptide': 612}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 591}
          Chain breaks: 3
    Chain: "T"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 761
          Classifications: {'DNA': 24}
          Modifications used: {'3*END': 1}
          Link IDs: {'rna3p': 23}
    Chain: "W"
      Number of atoms: 4574
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 142, 4574
          Classifications: {'RNA': 142}
          Modifications used: {'3*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 9, 'rna3p_pur': 69, 'rna3p_pyr': 50}
          Link IDs: {'rna2p': 23, 'rna3p': 118}
  Time building chain proxies: 2.30, per 1000 atoms: 0.15
  Number of scatterers: 15839
  At special positions: 0
  Unit cell: (81.549, 111.384, 166.413, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      38     16.00
     P     181     15.00
     O    2103      8.00
     N    1619      7.00
     C    4897      6.00
     H    7001      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: 1.30
  Conformation dependent library (CDL) restraints added in 281.3 milliseconds
  

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 3 sheets defined
      57.0% alpha, 8.8% beta
      54 base pairs and 93 stacking pairs defined.
    Time for finding SS restraints: 2.67
  Creating SS restraints...
    Processing helix  chain 'P' and resid 16 through 53
    Processing helix  chain 'P' and resid 65 through 77
    Processing helix  chain 'P' and resid 88 through 110
    Processing helix  chain 'P' and resid 114 through 119
    Processing helix  chain 'P' and resid 124 through 162
      removed outlier: 3.862A  pdb=" N   ALA P 129 " --> pdb=" O   SER P 125 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   TYR P 130 " --> pdb=" O   HIS P 126 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   SER P 131 " --> pdb=" O   VAL P 127 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   HIS P 146 " --> pdb=" O   ASN P 142 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER P 148 " --> pdb=" O   GLU P 144 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LYS P 149 " --> pdb=" O   ALA P 145 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR P 150 " --> pdb=" O   HIS P 146 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 165 through 182
    Processing helix  chain 'P' and resid 217 through 222
      removed outlier: 3.943A  pdb=" N   ASP P 221 " --> pdb=" O   PRO P 217 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU P 222 " --> pdb=" O   ARG P 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 217 through 222'
    Processing helix  chain 'P' and resid 225 through 228
    Processing helix  chain 'P' and resid 229 through 243
    Processing helix  chain 'P' and resid 273 through 281
    Processing helix  chain 'P' and resid 282 through 298
      removed outlier: 4.355A  pdb=" N   ASP P 288 " --> pdb=" O   ASP P 284 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 312 through 318
    Processing helix  chain 'P' and resid 323 through 339
      removed outlier: 3.621A  pdb=" N   ALA P 327 " --> pdb=" O   SER P 323 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 346 through 351
      removed outlier: 3.671A  pdb=" N   LEU P 350 " --> pdb=" O   GLN P 346 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 385 through 387
      No H-bonds generated for 'chain 'P' and resid 385 through 387'
    Processing helix  chain 'P' and resid 416 through 421
    Processing helix  chain 'P' and resid 447 through 454
    Processing helix  chain 'P' and resid 455 through 470
    Processing helix  chain 'P' and resid 472 through 479
    Processing helix  chain 'P' and resid 480 through 483
    Processing helix  chain 'P' and resid 489 through 512
      removed outlier: 3.729A  pdb=" N   TYR P 496 " --> pdb=" O   MET P 492 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG P 502 " --> pdb=" O   CYS P 498 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   MET P 503 " --> pdb=" O   SER P 499 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   HIS P 505 " --> pdb=" O   LYS P 501 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   MET P 506 " --> pdb=" O   ARG P 502 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 513 through 543
      removed outlier: 4.155A  pdb=" N   ARG P 517 " --> pdb=" O   HIS P 513 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR P 524 " --> pdb=" O   LYS P 520 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS P 528 " --> pdb=" O   TYR P 524 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER P 529 " --> pdb=" O   ASN P 525 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 556 through 564
    Processing helix  chain 'P' and resid 569 through 571
      No H-bonds generated for 'chain 'P' and resid 569 through 571'
    Processing helix  chain 'P' and resid 600 through 604
    Processing helix  chain 'P' and resid 657 through 670
    Processing sheet with id=AA1, first strand: chain 'P' and resid 4 through 10
      removed outlier: 6.995A  pdb=" N   SER P 376 " --> pdb=" O   VAL P 371 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   VAL P 371 " --> pdb=" O   SER P 376 " (cutoff:3.500A)
      removed outlier: 7.399A  pdb=" N   SER P 378 " --> pdb=" O   ALA P 369 " (cutoff:3.500A)
      removed outlier: 7.412A  pdb=" N   ALA P 369 " --> pdb=" O   SER P 378 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   GLN P 380 " --> pdb=" O   ASP P 367 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 442 through 446
      removed outlier: 6.298A  pdb=" N   LYS P 422 " --> pdb=" O   ILE P 574 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   GLY P 576 " --> pdb=" O   LYS P 422 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   LEU P 424 " --> pdb=" O   GLY P 576 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   GLY P 578 " --> pdb=" O   LEU P 424 " (cutoff:3.500A)
      removed outlier: 7.932A  pdb=" N   CYS P 426 " --> pdb=" O   GLY P 578 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 629 through 631

    258 hydrogen bonds defined for protein.
    762 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      138 hydrogen bonds
      268 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      93 stacking parallelities
  Total time for adding SS restraints: 3.05

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        0.94 -     1.11: 6984
        1.11 -     1.29: 958
        1.29 -     1.47: 4240
        1.47 -     1.64: 4163
        1.64 -     1.82: 59
  Bond restraints: 16404
  Sorted by residual:
  bond pdb=" C2    A W 137 "
       pdb=" H2    A W 137 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C5    U W  41 "
       pdb=" H5    U W  41 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C8    A W 141 "
       pdb=" H8    A W 141 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" C5    U W  20 "
       pdb=" H5    U W  20 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.67e+01
  bond pdb=" N   ASN P 114 "
       pdb=" H   ASN P 114 "
    ideal  model  delta    sigma   weight residual
    0.860  1.010 -0.150 2.00e-02 2.50e+03 5.66e+01
  ... (remaining 16399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.71: 25326
        2.71 -     5.41: 3384
        5.41 -     8.12: 726
        8.12 -    10.82: 37
       10.82 -    13.53: 20
  Bond angle restraints: 29493
  Sorted by residual:
  angle pdb=" O5'   U W  41 "
        pdb=" C5'   U W  41 "
        pdb=" C4'   U W  41 "
      ideal   model   delta    sigma   weight residual
     109.40  121.85  -12.45 8.00e-01 1.56e+00 2.42e+02
  angle pdb=" C4'   C W  81 "
        pdb=" O4'   C W  81 "
        pdb=" C1'   C W  81 "
      ideal   model   delta    sigma   weight residual
     109.70   99.16   10.54 7.00e-01 2.04e+00 2.27e+02
  angle pdb=" O4'   U W  41 "
        pdb=" C1'   U W  41 "
        pdb=" N1    U W  41 "
      ideal   model   delta    sigma   weight residual
     108.50  118.42   -9.92 7.00e-01 2.04e+00 2.01e+02
  angle pdb=" C4'   G W  79 "
        pdb=" O4'   G W  79 "
        pdb=" C1'   G W  79 "
      ideal   model   delta    sigma   weight residual
     109.70  100.22    9.48 7.00e-01 2.04e+00 1.83e+02
  angle pdb=" C5'   U W  41 "
        pdb=" C4'   U W  41 "
        pdb=" O4'   U W  41 "
      ideal   model   delta    sigma   weight residual
     109.80  121.75  -11.95 9.00e-01 1.23e+00 1.76e+02
  ... (remaining 29488 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.55: 6851
       33.55 -    67.10: 711
       67.10 -   100.65: 92
      100.65 -   134.19: 9
      134.19 -   167.74: 3
  Dihedral angle restraints: 7666
    sinusoidal: 5519
      harmonic: 2147
  Sorted by residual:
  dihedral pdb=" O4'   A W  53 "
           pdb=" C2'   A W  53 "
           pdb=" C1'   A W  53 "
           pdb=" C3'   A W  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -28.09   53.09     1      8.00e+00 1.56e-02 5.99e+01
  dihedral pdb=" C5'   G W  79 "
           pdb=" C4'   G W  79 "
           pdb=" C3'   G W  79 "
           pdb=" O3'   G W  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   94.16   52.84     1      8.00e+00 1.56e-02 5.94e+01
  dihedral pdb=" C3'   G W  45 "
           pdb=" C4'   G W  45 "
           pdb=" O4'   G W  45 "
           pdb=" C1'   G W  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
      20.00  -32.55   52.55     1      8.00e+00 1.56e-02 5.88e+01
  ... (remaining 7663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 1223
       0.105 -    0.210: 322
       0.210 -    0.315: 39
       0.315 -    0.420: 11
       0.420 -    0.525: 2
  Chirality restraints: 1597
  Sorted by residual:
  chirality pdb=" C4'   C W  81 "
            pdb=" C5'   C W  81 "
            pdb=" O4'   C W  81 "
            pdb=" C3'   C W  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -1.98   -0.53 2.00e-01 2.50e+01 6.90e+00
  chirality pdb=" C4'   A W  43 "
            pdb=" C5'   A W  43 "
            pdb=" O4'   A W  43 "
            pdb=" C3'   A W  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.06   -0.44 2.00e-01 2.50e+01 4.87e+00
  chirality pdb=" C4'   U W  41 "
            pdb=" C5'   U W  41 "
            pdb=" O4'   U W  41 "
            pdb=" C3'   U W  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.09   -0.40 2.00e-01 2.50e+01 4.07e+00
  ... (remaining 1594 not shown)

  Planarity restraints: 1785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W 110 "   -0.461 2.00e-02 2.50e+03   1.75e-01 1.07e+03
        pdb=" N9    G W 110 "    0.001 2.00e-02 2.50e+03
        pdb=" C8    G W 110 "    0.149 2.00e-02 2.50e+03
        pdb=" N7    G W 110 "    0.133 2.00e-02 2.50e+03
        pdb=" C5    G W 110 "    0.013 2.00e-02 2.50e+03
        pdb=" C6    G W 110 "   -0.112 2.00e-02 2.50e+03
        pdb=" O6    G W 110 "   -0.224 2.00e-02 2.50e+03
        pdb=" N1    G W 110 "   -0.057 2.00e-02 2.50e+03
        pdb=" C2    G W 110 "    0.047 2.00e-02 2.50e+03
        pdb=" N2    G W 110 "    0.246 2.00e-02 2.50e+03
        pdb=" N3    G W 110 "    0.056 2.00e-02 2.50e+03
        pdb=" C4    G W 110 "    0.041 2.00e-02 2.50e+03
        pdb=" H8    G W 110 "    0.204 2.00e-02 2.50e+03
        pdb=" H1    G W 110 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G W  71 "   -0.457 2.00e-02 2.50e+03   1.74e-01 1.06e+03
        pdb=" N9    G W  71 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    G W  71 "    0.156 2.00e-02 2.50e+03
        pdb=" N7    G W  71 "    0.049 2.00e-02 2.50e+03
        pdb=" C5    G W  71 "   -0.021 2.00e-02 2.50e+03
        pdb=" C6    G W  71 "   -0.109 2.00e-02 2.50e+03
        pdb=" O6    G W  71 "   -0.237 2.00e-02 2.50e+03
        pdb=" N1    G W  71 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2    G W  71 "    0.045 2.00e-02 2.50e+03
        pdb=" N2    G W  71 "    0.198 2.00e-02 2.50e+03
        pdb=" N3    G W  71 "    0.043 2.00e-02 2.50e+03
        pdb=" C4    G W  71 "    0.032 2.00e-02 2.50e+03
        pdb=" H8    G W  71 "    0.268 2.00e-02 2.50e+03
        pdb=" H1    G W  71 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C W  81 "    0.377 2.00e-02 2.50e+03   1.85e-01 9.43e+02
        pdb=" N1    C W  81 "    0.058 2.00e-02 2.50e+03
        pdb=" C2    C W  81 "   -0.054 2.00e-02 2.50e+03
        pdb=" O2    C W  81 "   -0.357 2.00e-02 2.50e+03
        pdb=" N3    C W  81 "    0.043 2.00e-02 2.50e+03
        pdb=" C4    C W  81 "    0.104 2.00e-02 2.50e+03
        pdb=" N4    C W  81 "    0.206 2.00e-02 2.50e+03
        pdb=" C5    C W  81 "   -0.052 2.00e-02 2.50e+03
        pdb=" C6    C W  81 "   -0.039 2.00e-02 2.50e+03
        pdb=" H5    C W  81 "   -0.164 2.00e-02 2.50e+03
        pdb=" H6    C W  81 "   -0.122 2.00e-02 2.50e+03
  ... (remaining 1782 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 770
        2.11 -     2.73: 20927
        2.73 -     3.35: 44014
        3.35 -     3.98: 58796
        3.98 -     4.60: 84987
  Nonbonded interactions: 209494
  Sorted by model distance:
  nonbonded pdb="HO2'   C W  78 "
            pdb=" H4'   G W  79 "
     model   vdw
     1.487 2.270
  nonbonded pdb="HO2'   G W  42 "
            pdb=" H4'   A W  43 "
     model   vdw
     1.507 2.270
  nonbonded pdb="HO2'   C W  81 "
            pdb=" OP1   A W  82 "
     model   vdw
     1.561 2.450
  nonbonded pdb="HO2'   A W 123 "
            pdb=" OP2   A W 124 "
     model   vdw
     1.563 2.450
  nonbonded pdb="HO2'   A W  82 "
            pdb=" OP2   U W  83 "
     model   vdw
     1.565 2.450
  ... (remaining 209489 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:             2.970
  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:             0.100
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     15.500
  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:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4619
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      :  0.014   0.057   9403  Z= 1.252
  Angle     :  1.980  13.527  13534  Z= 2.003
  Chirality :  0.095   0.525   1597
  Planarity :  0.034   0.180   1055
  Dihedral  : 23.225 167.742   4512
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 1.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  2.00 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.32), residues: 604
  helix: -0.39 (0.27), residues: 316
  sheet: -1.56 (0.62), residues: 40
  loop : -0.41 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG P 668 
 TYR   0.074   0.019   TYR P 445 
 PHE   0.054   0.012   PHE P 519 
 TRP   0.116   0.021   TRP P 654 
 HIS   0.012   0.003   HIS P 641 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01355 /  1.25 ( 9403)
  covalent geometry    : angle       1.97984 /  2.00 (13534)
  hydrogen bonds       : bond        0.14811 / 15.67 (  396)
  hydrogen bonds       : angle       7.94823 /  8.28 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  256 ASN cc_start: 0.5854 (t0) cc_final: 0.5475 (t0)
REVERT: P  272 ASP cc_start: 0.7284 (p0) cc_final: 0.7028 (p0)
REVERT: P  283 LYS cc_start: 0.7057 (tttt) cc_final: 0.6801 (tppt)
REVERT: P  492 MET cc_start: 0.6846 (mmm) cc_final: 0.6321 (tpt)
  outliers start: 5
  outliers final: 2
  residues processed: 134
  average time/residue: 0.2762
  time to fit residues: 45.3747
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  567 VAL
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4839 r_free = 0.4839 target = 0.232835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.191674 restraints weight = 32295.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.4417 rms_B_bonded: 2.86
r_work: 0.3958 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9403  Z= 0.240
  Angle     :  0.953  12.110  13534  Z= 0.577
  Chirality :  0.061   0.444   1597
  Planarity :  0.007   0.052   1055
  Dihedral  : 25.489 168.883   3246
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  :  9.09 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.34), residues: 604
  helix:  0.61 (0.28), residues: 322
  sheet: -2.22 (0.58), residues: 49
  loop : -0.19 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG P 345 
 TYR   0.015   0.002   TYR P  45 
 PHE   0.020   0.002   PHE P  67 
 TRP   0.021   0.002   TRP P 655 
 HIS   0.006   0.002   HIS P 615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.24 ( 9403)
  covalent geometry    : angle       0.95285 /  0.58 (13534)
  hydrogen bonds       : bond        0.09186 /  9.28 (  396)
  hydrogen bonds       : angle       5.11650 /  5.80 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7644 (mtt90) cc_final: 0.7352 (mmt90)
REVERT: P  140 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7954 (pttt)
REVERT: P  272 ASP cc_start: 0.8332 (p0) cc_final: 0.8000 (p0)
REVERT: P  484 GLN cc_start: 0.4945 (tp-100) cc_final: 0.4640 (pt0)
REVERT: P  492 MET cc_start: 0.7131 (mmm) cc_final: 0.6911 (tpt)
REVERT: P  567 VAL cc_start: 0.7460 (OUTLIER) cc_final: 0.7195 (t)
  outliers start: 11
  outliers final: 6
  residues processed: 82
  average time/residue: 0.1903
  time to fit residues: 21.6893
Evaluate side-chains
  69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   80 THR
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  567 VAL
Chi-restraints excluded: chain P residue  574 ILE
Chi-restraints excluded: chain P residue  654 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 61 optimal weight:    5.9990
   chunk 74 optimal weight:   50.0000
   chunk 26 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P  77 GLN
P 357 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.230434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.184004 restraints weight = 33585.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.4335 rms_B_bonded: 3.09
r_work: 0.3904 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9403  Z= 0.213
  Angle     :  0.811  10.512  13534  Z= 0.482
  Chirality :  0.054   0.425   1597
  Planarity :  0.006   0.060   1055
  Dihedral  : 25.292 168.043   3246
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  :  9.27 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.34), residues: 604
  helix:  0.76 (0.28), residues: 317
  sheet: -2.03 (0.60), residues: 51
  loop : -0.22 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P 602 
 TYR   0.023   0.002   TYR P 475 
 PHE   0.022   0.002   PHE P 366 
 TRP   0.009   0.002   TRP P 655 
 HIS   0.014   0.002   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.21 ( 9403)
  covalent geometry    : angle       0.81068 /  0.48 (13534)
  hydrogen bonds       : bond        0.08228 /  8.38 (  396)
  hydrogen bonds       : angle       4.75237 /  5.43 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  140 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7986 (pttt)
REVERT: P  272 ASP cc_start: 0.8367 (p0) cc_final: 0.8109 (p0)
  outliers start: 13
  outliers final: 10
  residues processed: 74
  average time/residue: 0.1756
  time to fit residues: 17.7090
Evaluate side-chains
  69 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   21 VAL
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  277 SER
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  323 SER
Chi-restraints excluded: chain P residue  504 GLU
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 72 optimal weight:   40.0000
   chunk 45 optimal weight:    0.5980
   chunk 65 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4827 r_free = 0.4827 target = 0.232067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.186175 restraints weight = 33435.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.4370 rms_B_bonded: 2.84
r_work: 0.3961 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.4135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9403  Z= 0.160
  Angle     :  0.699   9.909  13534  Z= 0.417
  Chirality :  0.049   0.396   1597
  Planarity :  0.005   0.051   1055
  Dihedral  : 25.120 162.064   3245
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.73 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.35), residues: 604
  helix:  1.36 (0.29), residues: 318
  sheet: -1.91 (0.63), residues: 53
  loop : -0.02 (0.44), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  42 
 TYR   0.016   0.001   TYR P 475 
 PHE   0.023   0.002   PHE P  67 
 TRP   0.010   0.001   TRP P 655 
 HIS   0.005   0.001   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.16 ( 9403)
  covalent geometry    : angle       0.69862 /  0.42 (13534)
  hydrogen bonds       : bond        0.07015 /  7.27 (  396)
  hydrogen bonds       : angle       4.36706 /  4.92 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  140 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7937 (pttt)
REVERT: P  256 ASN cc_start: 0.6899 (OUTLIER) cc_final: 0.6648 (t0)
REVERT: P  272 ASP cc_start: 0.8325 (p0) cc_final: 0.8104 (p0)
REVERT: P  559 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6348 (ttm)
  outliers start: 11
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1443
  time to fit residues: 14.1145
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    4 ILE
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  256 ASN
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  559 MET
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.3980
   chunk 44 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 11 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** P  68 HIS ** 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 = 0.4825 r_free = 0.4825 target = 0.231647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.185550 restraints weight = 33514.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.4366 rms_B_bonded: 2.89
r_work: 0.3948 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9403  Z= 0.157
  Angle     :  0.669   9.627  13534  Z= 0.398
  Chirality :  0.047   0.376   1597
  Planarity :  0.005   0.074   1055
  Dihedral  : 25.045 163.628   3245
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.27 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.35), residues: 604
  helix:  1.46 (0.29), residues: 318
  sheet: -1.81 (0.65), residues: 53
  loop : -0.08 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 602 
 TYR   0.010   0.001   TYR P  45 
 PHE   0.026   0.001   PHE P  67 
 TRP   0.007   0.001   TRP P 655 
 HIS   0.006   0.001   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.16 ( 9403)
  covalent geometry    : angle       0.66925 /  0.40 (13534)
  hydrogen bonds       : bond        0.06789 /  7.04 (  396)
  hydrogen bonds       : angle       4.34060 /  4.87 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  140 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7931 (pttt)
REVERT: P  272 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.8110 (p0)
REVERT: P  559 MET cc_start: 0.7048 (OUTLIER) cc_final: 0.6368 (ttm)
REVERT: P  561 MET cc_start: 0.7611 (mmm) cc_final: 0.7411 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.2131
  time to fit residues: 19.2496
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  272 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  559 MET
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 68 optimal weight:   10.0000
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    0.1980
   overall best weight:    1.3784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** P  68 HIS ** 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 = 0.4809 r_free = 0.4809 target = 0.229995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.185126 restraints weight = 33190.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.4346 rms_B_bonded: 3.14
r_work: 0.3878 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9403  Z= 0.173
  Angle     :  0.661   9.371  13534  Z= 0.387
  Chirality :  0.045   0.352   1597
  Planarity :  0.006   0.061   1055
  Dihedral  : 24.993 165.373   3245
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 11.82 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.35), residues: 604
  helix:  1.34 (0.29), residues: 318
  sheet: -1.99 (0.67), residues: 53
  loop : -0.18 (0.43), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG P  81 
 TYR   0.013   0.002   TYR P 105 
 PHE   0.021   0.002   PHE P  67 
 TRP   0.008   0.001   TRP P 655 
 HIS   0.005   0.001   HIS P 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.17 ( 9403)
  covalent geometry    : angle       0.66114 /  0.39 (13534)
  hydrogen bonds       : bond        0.06986 /  7.27 (  396)
  hydrogen bonds       : angle       4.34156 /  4.89 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7395 (mpt180)
REVERT: P  140 LYS cc_start: 0.8219 (mtpt) cc_final: 0.7960 (pttt)
REVERT: P  319 ARG cc_start: 0.7390 (ppt170) cc_final: 0.7074 (ppt170)
  outliers start: 10
  outliers final: 9
  residues processed: 72
  average time/residue: 0.1874
  time to fit residues: 18.1825
Evaluate side-chains
  72 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue    4 ILE
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  499 SER
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0870
   chunk 48 optimal weight:    0.3980
   chunk 64 optimal weight:    9.9990
   chunk 60 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 59 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6560

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.232082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.184962 restraints weight = 33401.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.4341 rms_B_bonded: 1.95
r_work: 0.4007 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9403  Z= 0.133
  Angle     :  0.609   9.001  13534  Z= 0.359
  Chirality :  0.043   0.352   1597
  Planarity :  0.005   0.046   1055
  Dihedral  : 24.987 174.522   3245
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.18 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.35), residues: 604
  helix:  1.64 (0.30), residues: 315
  sheet: -1.87 (0.65), residues: 58
  loop : -0.10 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 459 
 TYR   0.015   0.001   TYR P 176 
 PHE   0.026   0.001   PHE P  67 
 TRP   0.008   0.001   TRP P 655 
 HIS   0.007   0.001   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.13 ( 9403)
  covalent geometry    : angle       0.60926 /  0.36 (13534)
  hydrogen bonds       : bond        0.06231 /  6.58 (  396)
  hydrogen bonds       : angle       4.19187 /  4.71 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7717 (mmt-90) cc_final: 0.7319 (mpt180)
REVERT: P  319 ARG cc_start: 0.7315 (ppt170) cc_final: 0.7095 (ppt170)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1992
  time to fit residues: 17.4306
Evaluate side-chains
  68 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 64 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:   20.0000
   chunk 36 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 22 optimal weight:    0.7980
   chunk 57 optimal weight:    0.1980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** P  68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 568 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.230922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.177438 restraints weight = 33669.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.4254 rms_B_bonded: 1.84
r_work: 0.4021 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3879 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.5201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9403  Z= 0.151
  Angle     :  0.607   8.905  13534  Z= 0.355
  Chirality :  0.042   0.337   1597
  Planarity :  0.005   0.041   1055
  Dihedral  : 24.896 178.712   3245
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.36 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.35), residues: 604
  helix:  1.65 (0.29), residues: 315
  sheet: -1.91 (0.64), residues: 58
  loop : -0.15 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P 602 
 TYR   0.013   0.002   TYR P 176 
 PHE   0.019   0.002   PHE P  67 
 TRP   0.008   0.001   TRP P 655 
 HIS   0.005   0.001   HIS P 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.15 ( 9403)
  covalent geometry    : angle       0.60654 /  0.35 (13534)
  hydrogen bonds       : bond        0.06524 /  6.80 (  396)
  hydrogen bonds       : angle       4.19575 /  4.72 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7856 (mmt-90) cc_final: 0.7491 (mpt180)
REVERT: P  577 TRP cc_start: 0.7204 (m100) cc_final: 0.6968 (m100)
  outliers start: 7
  outliers final: 6
  residues processed: 68
  average time/residue: 0.1882
  time to fit residues: 17.1640
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Chi-restraints excluded: chain P residue  667 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 67 optimal weight:   10.0000
   chunk 75 optimal weight:   30.0000
   overall best weight:    1.1186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4818 r_free = 0.4818 target = 0.231185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.177497 restraints weight = 33418.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.4254 rms_B_bonded: 1.87
r_work: 0.4026 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3875 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7441
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9403  Z= 0.138
  Angle     :  0.586   8.716  13534  Z= 0.343
  Chirality :  0.041   0.333   1597
  Planarity :  0.005   0.038   1055
  Dihedral  : 24.850 179.084   3245
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 12.55 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.35), residues: 604
  helix:  1.71 (0.29), residues: 315
  sheet: -1.90 (0.64), residues: 58
  loop : -0.01 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P  42 
 TYR   0.022   0.002   TYR P  44 
 PHE   0.023   0.001   PHE P  67 
 TRP   0.008   0.001   TRP P 655 
 HIS   0.003   0.001   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.14 ( 9403)
  covalent geometry    : angle       0.58604 /  0.34 (13534)
  hydrogen bonds       : bond        0.06219 /  6.55 (  396)
  hydrogen bonds       : angle       4.14011 /  4.68 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7596 (mpt180)
REVERT: P  560 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7662 (mtm180)
REVERT: P  577 TRP cc_start: 0.7215 (m100) cc_final: 0.6977 (m100)
  outliers start: 5
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2169
  time to fit residues: 18.6126
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 65 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 61 optimal weight:    4.9990
   chunk 57 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 72 optimal weight:   40.0000
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
P 256 ASN
P 635 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4811 r_free = 0.4811 target = 0.230431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.184376 restraints weight = 33314.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 3.26
r_work: 0.3874 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9403  Z= 0.155
  Angle     :  0.594   8.539  13534  Z= 0.345
  Chirality :  0.041   0.332   1597
  Planarity :  0.005   0.039   1055
  Dihedral  : 24.799 178.437   3245
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.73 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.35), residues: 604
  helix:  1.73 (0.29), residues: 315
  sheet: -1.99 (0.63), residues: 58
  loop : -0.07 (0.44), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P 602 
 TYR   0.011   0.002   TYR P 105 
 PHE   0.019   0.002   PHE P  67 
 TRP   0.008   0.001   TRP P 655 
 HIS   0.005   0.001   HIS P 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.15 ( 9403)
  covalent geometry    : angle       0.59357 /  0.34 (13534)
  hydrogen bonds       : bond        0.06482 /  6.77 (  396)
  hydrogen bonds       : angle       4.18309 /  4.70 ( 1030)

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

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

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1208 Ramachandran restraints generated.
    604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 60
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P    5 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7673 (mpt180)
REVERT: P  577 TRP cc_start: 0.7205 (m100) cc_final: 0.6985 (m100)
  outliers start: 7
  outliers final: 6
  residues processed: 66
  average time/residue: 0.2113
  time to fit residues: 18.7793
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   43 SER
Chi-restraints excluded: chain P residue   96 ASP
Chi-restraints excluded: chain P residue  290 LYS
Chi-restraints excluded: chain P residue  538 VAL
Chi-restraints excluded: chain P residue  654 TRP
Chi-restraints excluded: chain P residue  655 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 24 optimal weight:    0.6980
   chunk 18 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 57 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 75 optimal weight:   20.0000
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.7180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4825 r_free = 0.4825 target = 0.232011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.179988 restraints weight = 33509.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.4284 rms_B_bonded: 2.05
r_work: 0.4017 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.5690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   9403  Z= 0.121
  Angle     :  0.557   8.249  13534  Z= 0.324
  Chirality :  0.040   0.331   1597
  Planarity :  0.004   0.037   1055
  Dihedral  : 24.735 179.064   3245
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 12.91 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.36), residues: 604
  helix:  1.93 (0.30), residues: 316
  sheet: -1.93 (0.68), residues: 53
  loop :  0.14 (0.44), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG P  42 
 TYR   0.010   0.001   TYR P  44 
 PHE   0.024   0.001   PHE P  67 
 TRP   0.009   0.001   TRP P 655 
 HIS   0.004   0.001   HIS P  68 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.12 ( 9403)
  covalent geometry    : angle       0.55698 /  0.32 (13534)
  hydrogen bonds       : bond        0.05908 /  6.20 (  396)
  hydrogen bonds       : angle       4.03724 /  4.55 ( 1030)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3841.02 seconds
wall clock time: 65 minutes 46.49 seconds (3946.49 seconds total)