Starting phenix.real_space_refine
on Sun Jul 27 05:56:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8csz_26976/07_2025/8csz_26976.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.028
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     236      5.49       5
     Mg      2      5.21       5
     S      27      5.16       5
     C    4741      2.51       5
     N    1654      2.21       5
     O    2287      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8948
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 3950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 494, 3950
          Classifications: {'peptide': 494}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 472}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 3937
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 3937
          Classifications: {'RNA': 184}
          Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 13, 'rna3p_pur': 91, 'rna3p_pyr': 67}
          Link IDs: {'rna2p': 25, 'rna3p': 158}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 661
          Classifications: {'DNA': 33}
          Link IDs: {'rna3p': 32}
    Chain: "E"
      Number of atoms: 397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 397
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2125  SG  CYS D 265      82.445  57.202  49.318  1.00 89.87           S

  Time building chain proxies: 6.17, per 1000 atoms: 0.69
  Number of scatterers: 8948
  At special positions: 0
  Unit cell: (99.51, 111.28, 131.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      27     16.00
     P     236     15.00
     Mg      2     11.99
     O    2287      8.00
     N    1654      7.00
     C    4741      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.59
  Conformation dependent library (CDL) restraints added in 468.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D 503 "
        pdb="ZN    ZN D 503 " - pdb=" SG  CYS D 265 "
        pdb="ZN    ZN D 503 " - pdb=" NE2 HIS D 268 "


  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 7 sheets defined
      34.8% alpha, 17.8% beta
      82 base pairs and 139 stacking pairs defined.
    Time for finding SS restraints: 3.76
  Creating SS restraints...
    Processing helix  chain 'D' and resid 21 through 29
    Processing helix  chain 'D' and resid 85 through 87
      No H-bonds generated for 'chain 'D' and resid 85 through 87'
    Processing helix  chain 'D' and resid 88 through 109
      removed outlier: 4.413A  pdb=" N   LYS D  92 " --> pdb=" O   LYS D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 109 through 121
    Processing helix  chain 'D' and resid 163 through 184
      removed outlier: 3.723A  pdb=" N   ILE D 183 " --> pdb=" O   LYS D 179 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 207 through 212
    Processing helix  chain 'D' and resid 221 through 230
    Processing helix  chain 'D' and resid 265 through 275
    Processing helix  chain 'D' and resid 275 through 286
      removed outlier: 3.715A  pdb=" N   GLU D 279 " --> pdb=" O   ASP D 275 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 294 through 314
      removed outlier: 3.870A  pdb=" N   VAL D 298 " --> pdb=" O   HIS D 294 " (cutoff:3.500A)
      Proline residue:  D 304  - end of helix
    Processing helix  chain 'D' and resid 323 through 334
    Processing helix  chain 'D' and resid 340 through 351
      removed outlier: 3.692A  pdb=" N   TYR D 344 " --> pdb=" O   TYR D 340 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA D 350 " --> pdb=" O   ILE D 346 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LEU D 351 " --> pdb=" O   ALA D 347 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 408 through 416
    Processing helix  chain 'D' and resid 417 through 423
    Processing helix  chain 'D' and resid 480 through 482
      No H-bonds generated for 'chain 'D' and resid 480 through 482'
    Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 17
      removed outlier: 5.180A  pdb=" N   MET D  15 " --> pdb=" O   VAL D   6 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   VAL D   6 " --> pdb=" O   MET D  15 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   TYR D   5 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LEU D  44 " --> pdb=" O   TYR D   5 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE D   7 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   THR D  41 " --> pdb=" O   VAL D  35 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 318 through 322
      removed outlier: 3.988A  pdb=" N   MET D  68 " --> pdb=" O   ALA D  81 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE D  79 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 129 through 131
    Processing sheet with id=AA4, first strand: chain 'D' and resid 243 through 246
    Processing sheet with id=AA5, first strand: chain 'D' and resid 378 through 380
      removed outlier: 6.593A  pdb=" N   GLN D 432 " --> pdb=" O   HIS D 379 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 392 through 395
      removed outlier: 5.883A  pdb=" N   LEU D 393 " --> pdb=" O   MET D 389 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   MET D 389 " --> pdb=" O   LEU D 393 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ALA D 395 " --> pdb=" O   TYR D 387 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER D 386 " --> pdb=" O   LYS D 427 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 476 through 478
      removed outlier: 6.997A  pdb=" N   GLY D 460 " --> pdb=" O   ASN D 467 " (cutoff:3.500A)
      removed outlier: 7.046A  pdb=" N   PHE D 469 " --> pdb=" O   SER D 458 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   SER D 458 " --> pdb=" O   PHE D 469 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   SER D 471 " --> pdb=" O   SER D 456 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   SER D 456 " --> pdb=" O   SER D 471 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   ILE D 444 " --> pdb=" O   LEU D 485 " (cutoff:3.500A)

    156 hydrogen bonds defined for protein.
    429 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      208 hydrogen bonds
      388 hydrogen bond angles
      0 basepair planarities
      82 basepair parallelities
      139 stacking parallelities
  Total time for adding SS restraints: 3.87

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1542
        1.33 -     1.45: 3518
        1.45 -     1.57: 4051
        1.57 -     1.69: 467
        1.69 -     1.80: 42
  Bond restraints: 9620
  Sorted by residual:
  bond pdb=" O5'   G C 172 "
       pdb=" C5'   G C 172 "
    ideal  model  delta    sigma   weight residual
    1.420  1.443 -0.023 1.50e-02 4.44e+03 2.29e+00
  bond pdb=" O5'   A C  78 "
       pdb=" C5'   A C  78 "
    ideal  model  delta    sigma   weight residual
    1.420  1.440 -0.020 1.50e-02 4.44e+03 1.73e+00
  bond pdb=" CB  ARG D 101 "
       pdb=" CG  ARG D 101 "
    ideal  model  delta    sigma   weight residual
    1.520  1.484  0.036 3.00e-02 1.11e+03 1.47e+00
  bond pdb=" N   ASN D 203 "
       pdb=" CA  ASN D 203 "
    ideal  model  delta    sigma   weight residual
    1.463  1.451  0.011 9.30e-03 1.16e+04 1.47e+00
  bond pdb=" O5'   U C 205 "
       pdb=" C5'   U C 205 "
    ideal  model  delta    sigma   weight residual
    1.420  1.438 -0.018 1.50e-02 4.44e+03 1.47e+00
  ... (remaining 9615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 13569
        1.54 -     3.08: 460
        3.08 -     4.62: 57
        4.62 -     6.16: 11
        6.16 -     7.70: 5
  Bond angle restraints: 14102
  Sorted by residual:
  angle pdb=" O3'  DG E 127 "
        pdb=" C3'  DG E 127 "
        pdb=" C2'  DG E 127 "
      ideal   model   delta    sigma   weight residual
     111.50  104.54    6.96 1.50e+00 4.44e-01 2.15e+01
  angle pdb=" C4'   U C 206 "
        pdb=" C3'   U C 206 "
        pdb=" O3'   U C 206 "
      ideal   model   delta    sigma   weight residual
     109.40  114.83   -5.43 1.50e+00 4.44e-01 1.31e+01
  angle pdb=" O3'  DA B  10 "
        pdb=" C3'  DA B  10 "
        pdb=" C2'  DA B  10 "
      ideal   model   delta    sigma   weight residual
     111.50  106.22    5.28 1.50e+00 4.44e-01 1.24e+01
  angle pdb=" C3'   A C 128 "
        pdb=" O3'   A C 128 "
        pdb=" P     U C 129 "
      ideal   model   delta    sigma   weight residual
     120.20  124.99   -4.79 1.50e+00 4.44e-01 1.02e+01
  angle pdb=" C4'   A C 128 "
        pdb=" C3'   A C 128 "
        pdb=" O3'   A C 128 "
      ideal   model   delta    sigma   weight residual
     109.40  114.19   -4.79 1.50e+00 4.44e-01 1.02e+01
  ... (remaining 14097 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.92: 5157
       34.92 -    69.84: 614
       69.84 -   104.77: 59
      104.77 -   139.69: 6
      139.69 -   174.61: 8
  Dihedral angle restraints: 5844
    sinusoidal: 4409
      harmonic: 1435
  Sorted by residual:
  dihedral pdb=" O4'   C C  60 "
           pdb=" C1'   C C  60 "
           pdb=" N1    C C  60 "
           pdb=" C2    C C  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   40.92  159.08     1      1.50e+01 4.44e-03 8.25e+01
  dihedral pdb=" O4'   C C  94 "
           pdb=" C1'   C C  94 "
           pdb=" N1    C C  94 "
           pdb=" C2    C C  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   57.39  174.61     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" O4'   U C 107 "
           pdb=" C1'   U C 107 "
           pdb=" N1    U C 107 "
           pdb=" C2    U C 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   39.42 -167.42     1      1.70e+01 3.46e-03 6.56e+01
  ... (remaining 5841 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1544
       0.062 -    0.124: 138
       0.124 -    0.185: 15
       0.185 -    0.247: 7
       0.247 -    0.309: 1
  Chirality restraints: 1705
  Sorted by residual:
  chirality pdb=" C3'   U C 206 "
            pdb=" C4'   U C 206 "
            pdb=" O3'   U C 206 "
            pdb=" C2'   U C 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.44   -0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" C3'   A C  78 "
            pdb=" C4'   A C  78 "
            pdb=" O3'   A C  78 "
            pdb=" C2'   A C  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.72    0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" C3'   A C 128 "
            pdb=" C4'   A C 128 "
            pdb=" O3'   A C 128 "
            pdb=" C2'   A C 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.52   -0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1702 not shown)

  Planarity restraints: 938
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C 122 "    0.036 2.00e-02 2.50e+03   1.63e-02 7.31e+00
        pdb=" N9    A C 122 "   -0.038 2.00e-02 2.50e+03
        pdb=" C8    A C 122 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A C 122 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A C 122 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A C 122 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A C 122 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A C 122 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A C 122 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A C 122 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    A C 122 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  91 "   -0.032 2.00e-02 2.50e+03   1.40e-02 5.86e+00
        pdb=" N9    G C  91 "    0.034 2.00e-02 2.50e+03
        pdb=" C8    G C  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    G C  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G C  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6    G C  91 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G C  91 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N2    G C  91 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    G C  91 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G C  91 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C C 127 "   -0.030 2.00e-02 2.50e+03   1.56e-02 5.47e+00
        pdb=" N1    C C 127 "    0.034 2.00e-02 2.50e+03
        pdb=" C2    C C 127 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C C 127 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C C 127 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    C C 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4    C C 127 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    C C 127 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    C C 127 "    0.003 2.00e-02 2.50e+03
  ... (remaining 935 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 61
        2.55 -     3.14: 6562
        3.14 -     3.72: 16549
        3.72 -     4.31: 23135
        4.31 -     4.90: 32429
  Nonbonded interactions: 78736
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS D 245 "
            pdb="MG    MG D 501 "
     model   vdw
     1.962 2.250
  nonbonded pdb=" NE2 HIS D 269 "
            pdb="MG    MG D 501 "
     model   vdw
     2.018 2.250
  nonbonded pdb=" OP2  DC E 111 "
            pdb="MG    MG D 502 "
     model   vdw
     2.021 2.170
  nonbonded pdb=" ND1 HIS D 273 "
            pdb="MG    MG D 501 "
     model   vdw
     2.071 2.250
  nonbonded pdb=" O2'   U C 180 "
            pdb=" OP1   C C 181 "
     model   vdw
     2.127 3.040
  ... (remaining 78731 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     28.640
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
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      :  0.006   0.340   9622  Z= 0.281
  Angle     :  0.672   7.704  14102  Z= 0.385
  Chirality :  0.040   0.309   1705
  Planarity :  0.004   0.053    938
  Dihedral  : 23.812 174.610   4922
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.37), residues: 492
  helix:  0.82 (0.42), residues: 152
  sheet: -1.55 (0.65), residues: 65
  loop : -1.27 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP D 478 
 HIS   0.007   0.001   HIS D 273 
 PHE   0.007   0.001   PHE D 453 
 TYR   0.011   0.002   TYR D 340 
 ARG   0.008   0.001   ARG D 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12252 (  364)
  hydrogen bonds       : angle       5.85488 (  817)
  metal coordination   : bond        0.24074 (    2)
  covalent geometry    : bond        0.00518 ( 9620)
  covalent geometry    : angle       0.67154 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.977 
Fit side-chains
REVERT: D  353 ASP cc_start: 0.7944 (m-30) cc_final: 0.7581 (p0)
REVERT: D  403 ASP cc_start: 0.7862 (m-30) cc_final: 0.7354 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 36
  average time/residue: 0.3881
  time to fit residues: 18.4146
Evaluate side-chains
  27 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 36 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    2.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.081581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.059340 restraints weight = 23987.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.60
r_work: 0.2840 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2732 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.0835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   9622  Z= 0.253
  Angle     :  0.645  11.032  14102  Z= 0.347
  Chirality :  0.038   0.260   1705
  Planarity :  0.005   0.048    938
  Dihedral  : 24.809 175.625   3920
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.18 %
    Favored  : 94.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.37), residues: 492
  helix:  1.13 (0.42), residues: 152
  sheet: -1.41 (0.65), residues: 61
  loop : -1.06 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 161 
 HIS   0.011   0.001   HIS D 268 
 PHE   0.009   0.001   PHE D 453 
 TYR   0.012   0.002   TYR D   5 
 ARG   0.005   0.001   ARG D 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05079 (  364)
  hydrogen bonds       : angle       3.87910 (  817)
  metal coordination   : bond        0.00775 (    2)
  covalent geometry    : bond        0.00521 ( 9620)
  covalent geometry    : angle       0.64508 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.657 
Fit side-chains
REVERT: D  208 ARG cc_start: 0.7494 (mpp80) cc_final: 0.6544 (mtp180)
REVERT: D  273 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7257 (t70)
REVERT: D  353 ASP cc_start: 0.8645 (m-30) cc_final: 0.7917 (p0)
REVERT: D  403 ASP cc_start: 0.8294 (m-30) cc_final: 0.7423 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 33
  average time/residue: 0.3883
  time to fit residues: 18.1788
Evaluate side-chains
  30 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  273 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0980
   chunk 50 optimal weight:    4.9990
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:   20.0000
   chunk 46 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    5.9990
   chunk 31 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.082025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.059954 restraints weight = 24172.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 1.65
r_work: 0.2813 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9622  Z= 0.178
  Angle     :  0.581   9.330  14102  Z= 0.314
  Chirality :  0.035   0.210   1705
  Planarity :  0.004   0.046    938
  Dihedral  : 24.651 177.977   3920
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  7.53 %
    Favored  : 91.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.37), residues: 492
  helix:  1.43 (0.42), residues: 154
  sheet: -1.00 (0.68), residues: 55
  loop : -1.04 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 273 
 PHE   0.007   0.001   PHE D 453 
 TYR   0.010   0.001   TYR D   5 
 ARG   0.004   0.001   ARG D 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04341 (  364)
  hydrogen bonds       : angle       3.62932 (  817)
  metal coordination   : bond        0.00124 (    2)
  covalent geometry    : bond        0.00364 ( 9620)
  covalent geometry    : angle       0.58147 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.564 
Fit side-chains
REVERT: D  353 ASP cc_start: 0.8667 (m-30) cc_final: 0.7997 (p0)
REVERT: D  389 MET cc_start: 0.8328 (tpp) cc_final: 0.8120 (tpp)
  outliers start: 6
  outliers final: 3
  residues processed: 38
  average time/residue: 0.2964
  time to fit residues: 14.9367
Evaluate side-chains
  31 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 28
  time to evaluate  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.079521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.057337 restraints weight = 24188.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.2865 rms_B_bonded: 1.73
r_work: 0.2748 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038   9622  Z= 0.314
  Angle     :  0.662  10.507  14102  Z= 0.353
  Chirality :  0.040   0.291   1705
  Planarity :  0.005   0.041    938
  Dihedral  : 24.686 177.818   3920
  Min Nonbonded Distance : 1.537

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  8.47 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.37), residues: 492
  helix:  1.17 (0.42), residues: 152
  sheet: -1.23 (0.67), residues: 55
  loop : -1.10 (0.35), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 161 
 HIS   0.007   0.001   HIS D 273 
 PHE   0.010   0.001   PHE D 453 
 TYR   0.012   0.002   TYR D   5 
 ARG   0.005   0.001   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05298 (  364)
  hydrogen bonds       : angle       3.74360 (  817)
  metal coordination   : bond        0.00274 (    2)
  covalent geometry    : bond        0.00651 ( 9620)
  covalent geometry    : angle       0.66165 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.632 
Fit side-chains
REVERT: D  208 ARG cc_start: 0.7484 (mpp80) cc_final: 0.6533 (mtp180)
REVERT: D  353 ASP cc_start: 0.8669 (m-30) cc_final: 0.7793 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 34
  average time/residue: 0.2882
  time to fit residues: 13.2403
Evaluate side-chains
  32 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 28
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   chunk 41 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.8986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.079732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.057581 restraints weight = 24169.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.72
r_work: 0.2757 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2650 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8711
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   9622  Z= 0.286
  Angle     :  0.641  10.355  14102  Z= 0.343
  Chirality :  0.039   0.280   1705
  Planarity :  0.004   0.040    938
  Dihedral  : 24.627 178.057   3920
  Min Nonbonded Distance : 1.585

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  9.88 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.37), residues: 492
  helix:  1.15 (0.42), residues: 152
  sheet: -1.06 (0.65), residues: 60
  loop : -1.11 (0.36), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 161 
 HIS   0.007   0.001   HIS D 273 
 PHE   0.009   0.001   PHE D 453 
 TYR   0.012   0.002   TYR D   5 
 ARG   0.006   0.001   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04999 (  364)
  hydrogen bonds       : angle       3.73399 (  817)
  metal coordination   : bond        0.00180 (    2)
  covalent geometry    : bond        0.00590 ( 9620)
  covalent geometry    : angle       0.64103 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.698 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8643 (mtm) cc_final: 0.8197 (ttp)
REVERT: D  208 ARG cc_start: 0.7471 (mpp80) cc_final: 0.6511 (mtp180)
REVERT: D  353 ASP cc_start: 0.8696 (m-30) cc_final: 0.7892 (p0)
  outliers start: 7
  outliers final: 7
  residues processed: 34
  average time/residue: 0.4251
  time to fit residues: 19.1429
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 32 optimal weight:    6.9990
   chunk 42 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 57 optimal weight:    5.9990
   chunk 64 optimal weight:    6.9990
   chunk 68 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    2.3184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.080528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.058427 restraints weight = 24033.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2895 rms_B_bonded: 1.70
r_work: 0.2778 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   9622  Z= 0.236
  Angle     :  0.603   9.272  14102  Z= 0.324
  Chirality :  0.037   0.239   1705
  Planarity :  0.004   0.039    938
  Dihedral  : 24.537 179.744   3920
  Min Nonbonded Distance : 1.592

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.35 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.37), residues: 492
  helix:  1.27 (0.42), residues: 152
  sheet: -1.10 (0.69), residues: 55
  loop : -1.02 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 269 
 PHE   0.008   0.001   PHE D 453 
 TYR   0.011   0.001   TYR D   5 
 ARG   0.004   0.001   ARG D 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04547 (  364)
  hydrogen bonds       : angle       3.65485 (  817)
  metal coordination   : bond        0.00144 (    2)
  covalent geometry    : bond        0.00486 ( 9620)
  covalent geometry    : angle       0.60279 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 30
  time to evaluate  : 0.517 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8642 (mtm) cc_final: 0.8236 (ttp)
REVERT: D  208 ARG cc_start: 0.7385 (mpp80) cc_final: 0.6380 (mtp180)
REVERT: D  353 ASP cc_start: 0.8691 (m-30) cc_final: 0.7902 (p0)
  outliers start: 7
  outliers final: 7
  residues processed: 36
  average time/residue: 0.3197
  time to fit residues: 15.3357
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.081183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.059061 restraints weight = 24341.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 1.62
r_work: 0.2795 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9622  Z= 0.195
  Angle     :  0.578   8.250  14102  Z= 0.312
  Chirality :  0.035   0.214   1705
  Planarity :  0.004   0.039    938
  Dihedral  : 24.458 179.402   3920
  Min Nonbonded Distance : 1.615

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.59 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.38), residues: 492
  helix:  1.42 (0.42), residues: 154
  sheet: -1.02 (0.68), residues: 55
  loop : -0.97 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 478 
 HIS   0.004   0.001   HIS D 273 
 PHE   0.008   0.001   PHE D  79 
 TYR   0.011   0.001   TYR D   5 
 ARG   0.005   0.000   ARG D 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04243 (  364)
  hydrogen bonds       : angle       3.55970 (  817)
  metal coordination   : bond        0.00110 (    2)
  covalent geometry    : bond        0.00402 ( 9620)
  covalent geometry    : angle       0.57828 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.612 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8619 (mtm) cc_final: 0.8272 (ttp)
REVERT: D  208 ARG cc_start: 0.7350 (mpp80) cc_final: 0.6357 (mtp180)
REVERT: D  353 ASP cc_start: 0.8687 (m-30) cc_final: 0.7909 (p0)
REVERT: D  389 MET cc_start: 0.8236 (tpp) cc_final: 0.7916 (tpp)
  outliers start: 8
  outliers final: 8
  residues processed: 34
  average time/residue: 0.4397
  time to fit residues: 20.3538
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0980
   chunk 24 optimal weight:    0.0570
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    9.9990
   overall best weight:    2.2304

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.080447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.058374 restraints weight = 24327.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.73
r_work: 0.2774 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   9622  Z= 0.232
  Angle     :  0.597   8.042  14102  Z= 0.321
  Chirality :  0.036   0.249   1705
  Planarity :  0.004   0.038    938
  Dihedral  : 24.424 178.674   3920
  Min Nonbonded Distance : 1.585

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.35 %
    Favored  : 87.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.38), residues: 492
  helix:  1.41 (0.42), residues: 152
  sheet: -1.11 (0.68), residues: 55
  loop : -0.97 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 273 
 PHE   0.008   0.001   PHE D 453 
 TYR   0.012   0.001   TYR D   5 
 ARG   0.004   0.000   ARG D 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  364)
  hydrogen bonds       : angle       3.58487 (  817)
  metal coordination   : bond        0.00148 (    2)
  covalent geometry    : bond        0.00479 ( 9620)
  covalent geometry    : angle       0.59682 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.808 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8692 (mtm) cc_final: 0.8343 (ttp)
REVERT: D  208 ARG cc_start: 0.7386 (mpp80) cc_final: 0.6382 (mtp180)
REVERT: D  353 ASP cc_start: 0.8732 (m-30) cc_final: 0.7942 (p0)
  outliers start: 9
  outliers final: 8
  residues processed: 35
  average time/residue: 0.4618
  time to fit residues: 21.9582
Evaluate side-chains
  36 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 28
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.080589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.058334 restraints weight = 24276.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 1.73
r_work: 0.2777 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2668 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.1616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   9622  Z= 0.229
  Angle     :  0.596   8.009  14102  Z= 0.320
  Chirality :  0.036   0.245   1705
  Planarity :  0.004   0.038    938
  Dihedral  : 24.405 178.688   3920
  Min Nonbonded Distance : 1.592

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.59 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.38), residues: 492
  helix:  1.43 (0.42), residues: 152
  sheet: -1.03 (0.69), residues: 55
  loop : -0.95 (0.37), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 161 
 HIS   0.004   0.001   HIS D 273 
 PHE   0.008   0.001   PHE D 453 
 TYR   0.012   0.001   TYR D   5 
 ARG   0.004   0.000   ARG D 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  364)
  hydrogen bonds       : angle       3.56496 (  817)
  metal coordination   : bond        0.00144 (    2)
  covalent geometry    : bond        0.00474 ( 9620)
  covalent geometry    : angle       0.59633 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.639 
Fit side-chains
REVERT: D  201 MET cc_start: 0.8661 (mtm) cc_final: 0.8339 (ttp)
REVERT: D  208 ARG cc_start: 0.7357 (mpp80) cc_final: 0.6357 (mtp180)
REVERT: D  353 ASP cc_start: 0.8722 (m-30) cc_final: 0.7969 (p0)
  outliers start: 9
  outliers final: 9
  residues processed: 34
  average time/residue: 0.3695
  time to fit residues: 16.4535
Evaluate side-chains
  37 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 28
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9990
   chunk 25 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 52 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.9202

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.082652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.060629 restraints weight = 23986.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.64
r_work: 0.2827 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2714 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8638
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9622  Z= 0.139
  Angle     :  0.541   7.825  14102  Z= 0.291
  Chirality :  0.033   0.193   1705
  Planarity :  0.004   0.038    938
  Dihedral  : 24.307 178.099   3920
  Min Nonbonded Distance : 1.665

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.82 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.38), residues: 492
  helix:  1.66 (0.43), residues: 154
  sheet: -0.90 (0.68), residues: 55
  loop : -0.89 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 478 
 HIS   0.002   0.001   HIS D 104 
 PHE   0.007   0.001   PHE D  79 
 TYR   0.010   0.001   TYR D 484 
 ARG   0.004   0.000   ARG D 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  364)
  hydrogen bonds       : angle       3.41960 (  817)
  metal coordination   : bond        0.00067 (    2)
  covalent geometry    : bond        0.00282 ( 9620)
  covalent geometry    : angle       0.54056 (14102)

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

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

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  984 Ramachandran restraints generated.
    492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 29
  time to evaluate  : 0.659 
Fit side-chains
REVERT: D  195 ARG cc_start: 0.8390 (mtm180) cc_final: 0.8044 (mtm180)
REVERT: D  201 MET cc_start: 0.8603 (mtm) cc_final: 0.8318 (ttp)
REVERT: D  353 ASP cc_start: 0.8697 (m-30) cc_final: 0.7920 (p0)
  outliers start: 9
  outliers final: 8
  residues processed: 35
  average time/residue: 0.2716
  time to fit residues: 13.1518
Evaluate side-chains
  35 residues out of total 428 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 27
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain D residue   68 MET
Chi-restraints excluded: chain D residue  228 MET
Chi-restraints excluded: chain D residue  237 CYS
Chi-restraints excluded: chain D residue  239 HIS
Chi-restraints excluded: chain D residue  273 HIS
Chi-restraints excluded: chain D residue  396 THR
Chi-restraints excluded: chain D residue  426 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 9 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    2.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.080222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.057972 restraints weight = 24019.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.2881 rms_B_bonded: 1.73
r_work: 0.2762 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   9622  Z= 0.258
  Angle     :  0.606   8.006  14102  Z= 0.325
  Chirality :  0.037   0.250   1705
  Planarity :  0.004   0.037    938
  Dihedral  : 24.365 177.699   3920
  Min Nonbonded Distance : 1.575

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.06 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.38), residues: 492
  helix:  1.46 (0.43), residues: 152
  sheet: -0.78 (0.63), residues: 65
  loop : -1.04 (0.37), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 161 
 HIS   0.005   0.001   HIS D 273 
 PHE   0.008   0.001   PHE D 453 
 TYR   0.013   0.001   TYR D   5 
 ARG   0.003   0.001   ARG D 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04672 (  364)
  hydrogen bonds       : angle       3.57464 (  817)
  metal coordination   : bond        0.00206 (    2)
  covalent geometry    : bond        0.00534 ( 9620)
  covalent geometry    : angle       0.60586 (14102)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5257.30 seconds
wall clock time: 97 minutes 26.25 seconds (5846.25 seconds total)