Starting phenix.real_space_refine
on Tue Aug  4 19:04:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z2t_73777/08_2026/9z2t_73777.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      56      5.49       5
     S      31      5.16       5
     C    3617      2.51       5
     N    1043      2.21       5
     O    1274      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 6021
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4802
          Classifications: {'peptide': 595}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 554}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 1192
          Classifications: {'RNA': 56}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 22, 'rna3p_pyr': 27}
          Link IDs: {'rna2p': 7, 'rna3p': 48}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.27, per 1000 atoms: 0.21
  Number of scatterers: 6021
  At special positions: 0
  Unit cell: (70.848, 83.64, 106.272, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      31     16.00
     P      56     15.00
     O    1274      8.00
     N    1043      7.00
     C    3617      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: 0.32
  Conformation dependent library (CDL) restraints added in 317.4 milliseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1130

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      41.5% alpha, 17.6% beta
      17 base pairs and 25 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 62 through 71
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 121 through 124
      removed outlier: 3.679A  pdb=" N   GLU A 124 " --> pdb=" O   TYR A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 124'
    Processing helix  chain 'A' and resid 133 through 139
    Processing helix  chain 'A' and resid 142 through 155
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 173
      removed outlier: 3.510A  pdb=" N   LEU A 170 " --> pdb=" O   MET A 166 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ASN A 173 " --> pdb=" O   PRO A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 4.035A  pdb=" N   GLN A 193 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 229
    Processing helix  chain 'A' and resid 242 through 246
      removed outlier: 3.800A  pdb=" N   ILE A 246 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 277
      removed outlier: 3.833A  pdb=" N   MET A 277 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 287
    Processing helix  chain 'A' and resid 289 through 309
      removed outlier: 4.595A  pdb=" N   GLY A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   LEU A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 340
      removed outlier: 4.034A  pdb=" N   ILE A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 380
    Processing helix  chain 'A' and resid 381 through 385
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.723A  pdb=" N   HIS A 405 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 408
      No H-bonds generated for 'chain 'A' and resid 406 through 408'
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 4.464A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 538
      removed outlier: 3.768A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 546
      No H-bonds generated for 'chain 'A' and resid 544 through 546'
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 607 through 612
    Processing helix  chain 'A' and resid 613 through 615
      No H-bonds generated for 'chain 'A' and resid 613 through 615'
    Processing helix  chain 'A' and resid 623 through 633
    Processing helix  chain 'A' and resid 637 through 641
    Processing helix  chain 'A' and resid 642 through 650
    Processing helix  chain 'A' and resid 691 through 702
    Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 117
      removed outlier: 8.371A  pdb=" N   TRP A 127 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   ILE A  80 " --> pdb=" O   TRP A 127 " (cutoff:3.500A)
      removed outlier: 7.427A  pdb=" N   THR A 129 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
      removed outlier: 7.574A  pdb=" N   LEU A  78 " --> pdb=" O   THR A 129 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU A 131 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 106 through 107
    Processing sheet with id=AA3, first strand: chain 'A' and resid 343 through 345
      removed outlier: 3.502A  pdb=" N   PHE A 422 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 345
      removed outlier: 4.511A  pdb=" N   GLY A 314 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   ASP A 263 " --> pdb=" O   GLY A 313 " (cutoff:3.500A)
      removed outlier: 6.144A  pdb=" N   LYS A 179 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 7.969A  pdb=" N   LEU A 266 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   LEU A 181 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   ILE A 236 " --> pdb=" O   THR A 583 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 236 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL A 238 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 250 through 253
    Processing sheet with id=AA6, first strand: chain 'A' and resid 366 through 367
    Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 522
      removed outlier: 6.908A  pdb=" N   LEU A 560 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 619 through 622

    191 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      84 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      25 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1744
        1.34 -     1.46: 1409
        1.46 -     1.58: 2966
        1.58 -     1.70: 110
        1.70 -     1.81: 50
  Bond restraints: 6279
  Sorted by residual:
  bond pdb=" N1    C B  48 "
       pdb=" C2    C B  48 "
    ideal  model  delta    sigma   weight residual
    1.397  1.420 -0.023 1.00e-02 1.00e+04 5.49e+00
  bond pdb=" CD  SFG A 801 "
       pdb=" NE  SFG A 801 "
    ideal  model  delta    sigma   weight residual
    1.471  1.496 -0.025 2.00e-02 2.50e+03 1.62e+00
  bond pdb=" C2'   C B  48 "
       pdb=" C1'   C B  48 "
    ideal  model  delta    sigma   weight residual
    1.529  1.542 -0.013 1.10e-02 8.26e+03 1.37e+00
  bond pdb=" C3'   C B  48 "
       pdb=" C2'   C B  48 "
    ideal  model  delta    sigma   weight residual
    1.523  1.535 -0.012 1.10e-02 8.26e+03 1.11e+00
  bond pdb=" CA  SFG A 801 "
       pdb=" C   SFG A 801 "
    ideal  model  delta    sigma   weight residual
    1.553  1.533  0.020 2.00e-02 2.50e+03 1.03e+00
  ... (remaining 6274 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.27: 8445
        1.27 -     2.54: 214
        2.54 -     3.80: 104
        3.80 -     5.07: 6
        5.07 -     6.34: 4
  Bond angle restraints: 8773
  Sorted by residual:
  angle pdb=" O5'   G B  45 "
        pdb=" C5'   G B  45 "
        pdb=" C4'   G B  45 "
      ideal   model   delta    sigma   weight residual
     109.40  115.74   -6.34 8.00e-01 1.56e+00 6.28e+01
  angle pdb=" O4'   G B  46 "
        pdb=" C1'   G B  46 "
        pdb=" N9    G B  46 "
      ideal   model   delta    sigma   weight residual
     108.50  111.45   -2.95 7.00e-01 2.04e+00 1.78e+01
  angle pdb=" O4'   C B  48 "
        pdb=" C1'   C B  48 "
        pdb=" N1    C B  48 "
      ideal   model   delta    sigma   weight residual
     108.50  111.10   -2.60 7.00e-01 2.04e+00 1.38e+01
  angle pdb=" O5'   G B  30 "
        pdb=" C5'   G B  30 "
        pdb=" C4'   G B  30 "
      ideal   model   delta    sigma   weight residual
     109.40  112.25   -2.85 8.00e-01 1.56e+00 1.27e+01
  angle pdb=" C1'   G B  45 "
        pdb=" N9    G B  45 "
        pdb=" C8    G B  45 "
      ideal   model   delta    sigma   weight residual
     127.00  122.44    4.56 1.30e+00 5.92e-01 1.23e+01
  ... (remaining 8768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.68: 3698
       25.68 -    51.36: 157
       51.36 -    77.04: 88
       77.04 -   102.71: 2
      102.71 -   128.39: 1
  Dihedral angle restraints: 3946
    sinusoidal: 2207
      harmonic: 1739
  Sorted by residual:
  dihedral pdb=" O4'   C B  48 "
           pdb=" C1'   C B  48 "
           pdb=" N1    C B  48 "
           pdb=" C2    C B  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   71.61  128.39     1      1.50e+01 4.44e-03 6.92e+01
  dihedral pdb=" O4'   G B  45 "
           pdb=" C1'   G B  45 "
           pdb=" N9    G B  45 "
           pdb=" C4    G B  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -78.00  -20.65  -57.35     1      1.70e+01 3.46e-03 1.53e+01
  dihedral pdb=" CB  LYS A 579 "
           pdb=" CG  LYS A 579 "
           pdb=" CD  LYS A 579 "
           pdb=" CE  LYS A 579 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.81  -57.19     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 3943 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 698
       0.036 -    0.072: 177
       0.072 -    0.108: 64
       0.108 -    0.144: 66
       0.144 -    0.180: 6
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" C4'   G B  45 "
            pdb=" C5'   G B  45 "
            pdb=" O4'   G B  45 "
            pdb=" C3'   G B  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.32   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality pdb=" P     G B  46 "
            pdb=" OP1   G B  46 "
            pdb=" OP2   G B  46 "
            pdb=" O5'   G B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.59   -0.18 2.00e-01 2.50e+01 8.08e-01
  chirality pdb=" C2'   C B  48 "
            pdb=" C3'   C B  48 "
            pdb=" O2'   C B  48 "
            pdb=" C1'   C B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.78    0.16 2.00e-01 2.50e+01 6.61e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  46 "   -0.071 2.00e-02 2.50e+03   3.59e-02 3.87e+01
        pdb=" N9    G B  46 "    0.100 2.00e-02 2.50e+03
        pdb=" C8    G B  46 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    G B  46 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5    G B  46 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    G B  46 "   -0.010 2.00e-02 2.50e+03
        pdb=" O6    G B  46 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    G B  46 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G B  46 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G B  46 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    G B  46 "    0.007 2.00e-02 2.50e+03
        pdb=" C4    G B  46 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  45 "   -0.033 2.00e-02 2.50e+03   2.61e-02 2.04e+01
        pdb=" N9    G B  45 "    0.076 2.00e-02 2.50e+03
        pdb=" C8    G B  45 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    G B  45 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    G B  45 "   -0.007 2.00e-02 2.50e+03
        pdb=" C6    G B  45 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6    G B  45 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    G B  45 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    G B  45 "    0.004 2.00e-02 2.50e+03
        pdb=" N2    G B  45 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  45 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G B  45 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B  63 "    0.024 2.00e-02 2.50e+03   1.48e-02 4.91e+00
        pdb=" N1    C B  63 "   -0.031 2.00e-02 2.50e+03
        pdb=" C2    C B  63 "    0.015 2.00e-02 2.50e+03
        pdb=" O2    C B  63 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    C B  63 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    C B  63 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C B  63 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    C B  63 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    C B  63 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 913 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 1934
        2.85 -     3.36: 5308
        3.36 -     3.88: 10389
        3.88 -     4.39: 11598
        4.39 -     4.90: 18804
  Nonbonded interactions: 48033
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 301 "
            pdb=" OP1   G B  30 "
     model   vdw
     2.341 3.120
  nonbonded pdb=" OD2 ASP A 268 "
            pdb=" N   SFG A 801 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" OP2   U B  50 "
            pdb=" N2    G B  59 "
     model   vdw
     2.402 3.120
  nonbonded pdb=" N2    G B   5 "
            pdb=" O2    U B  68 "
     model   vdw
     2.417 3.120
  nonbonded pdb=" O   ILE A 246 "
            pdb=" NH2 ARG A 305 "
     model   vdw
     2.418 3.120
  ... (remaining 48028 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.480
  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:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:    8.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
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      :  0.002   0.025   6279  Z= 0.120
  Angle     :  0.549   6.339   8773  Z= 0.391
  Chirality :  0.049   0.180   1011
  Planarity :  0.004   0.036    916
  Dihedral  : 16.242 128.392   2816
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.15 (0.36), residues: 591
  helix:  2.31 (0.41), residues: 193
  sheet:  0.28 (0.51), residues: 107
  loop :  1.50 (0.38), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 248 
 TYR   0.006   0.001   TYR A  52 
 PHE   0.011   0.001   PHE A  48 
 TRP   0.004   0.001   TRP A 588 
 HIS   0.002   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00184 /  0.12 ( 6279)
  covalent geometry    : angle       0.54860 /  0.39 ( 8773)
  hydrogen bonds       : bond        0.17146 / 10.42 (  235)
  hydrogen bonds       : angle       5.66247 /  3.78 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 HIS cc_start: 0.7862 (m90) cc_final: 0.6422 (m90)
REVERT: A  249 LEU cc_start: 0.8650 (mt) cc_final: 0.8414 (mt)
REVERT: A  367 MET cc_start: 0.8667 (ttp) cc_final: 0.8412 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.0766
  time to fit residues: 6.5683
Evaluate side-chains
  36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 36
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0060
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:   30.0000
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    1.4000

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 178 HIS
A 240 ASN
A 416 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.087442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.059838 restraints weight = 20630.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061854 restraints weight = 10951.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.063187 restraints weight = 7724.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063773 restraints weight = 6382.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.064399 restraints weight = 5805.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6279  Z= 0.149
  Angle     :  0.534   6.370   8773  Z= 0.279
  Chirality :  0.040   0.166   1011
  Planarity :  0.005   0.043    916
  Dihedral  : 18.674 123.621   1579
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  4.30 %
    Favored  : 94.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  2.13 (0.36), residues: 591
  helix:  2.42 (0.41), residues: 192
  sheet: -0.05 (0.48), residues: 111
  loop :  1.56 (0.39), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 315 
 TYR   0.008   0.001   TYR A  52 
 PHE   0.011   0.001   PHE A 206 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.010   0.001   HIS A 697 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 ( 6279)
  covalent geometry    : angle       0.53396 /  0.28 ( 8773)
  hydrogen bonds       : bond        0.04390 /  2.79 (  235)
  hydrogen bonds       : angle       4.68019 /  3.20 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 38
  time to evaluate  : 0.221 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 41
  average time/residue: 0.0677
  time to fit residues: 3.7206
Evaluate side-chains
  32 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 30
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  236 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 59 optimal weight:   30.0000
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 63 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.086645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.058886 restraints weight = 20476.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.060890 restraints weight = 10863.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.062166 restraints weight = 7706.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062844 restraints weight = 6411.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062845 restraints weight = 5836.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.1914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6279  Z= 0.137
  Angle     :  0.510   6.778   8773  Z= 0.260
  Chirality :  0.038   0.152   1011
  Planarity :  0.004   0.043    916
  Dihedral  : 18.673 124.015   1579
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  6.36 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.90 (0.36), residues: 591
  helix:  2.05 (0.40), residues: 193
  sheet: -0.12 (0.48), residues: 111
  loop :  1.53 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 700 
 TYR   0.005   0.001   TYR A  51 
 PHE   0.011   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 435 
 HIS   0.004   0.001   HIS A 146 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.14 ( 6279)
  covalent geometry    : angle       0.50956 /  0.26 ( 8773)
  hydrogen bonds       : bond        0.04005 /  2.57 (  235)
  hydrogen bonds       : angle       4.45762 /  3.08 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.126 
Fit side-chains
REVERT: A  701 MET cc_start: 0.9140 (mtp) cc_final: 0.8921 (mtp)
  outliers start: 7
  outliers final: 5
  residues processed: 34
  average time/residue: 0.0533
  time to fit residues: 2.6731
Evaluate side-chains
  36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue   86 HIS
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  277 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 62 optimal weight:   20.0000
   chunk 43 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 61 optimal weight:   30.0000
   chunk 13 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   overall best weight:    2.0984

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.084818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.057007 restraints weight = 20750.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.058923 restraints weight = 11036.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.060164 restraints weight = 7862.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.060778 restraints weight = 6548.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.061289 restraints weight = 5958.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6279  Z= 0.187
  Angle     :  0.539   6.955   8773  Z= 0.272
  Chirality :  0.039   0.157   1011
  Planarity :  0.004   0.045    916
  Dihedral  : 18.725 122.772   1579
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  8.22 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.84 (0.36), residues: 591
  helix:  2.01 (0.40), residues: 192
  sheet: -0.25 (0.47), residues: 112
  loop :  1.54 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 545 
 TYR   0.009   0.001   TYR A  51 
 PHE   0.019   0.002   PHE A 145 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.004   0.001   HIS A  86 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 ( 6279)
  covalent geometry    : angle       0.53866 /  0.27 ( 8773)
  hydrogen bonds       : bond        0.04060 /  2.67 (  235)
  hydrogen bonds       : angle       4.37030 /  3.04 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A  701 MET cc_start: 0.9157 (mtp) cc_final: 0.8888 (mtp)
REVERT: A  702 MET cc_start: 0.8662 (mmm) cc_final: 0.8451 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0486
  time to fit residues: 2.4631
Evaluate side-chains
  33 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  277 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 15 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0770
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    0.6738

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.085776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.058051 restraints weight = 20718.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.060011 restraints weight = 10853.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.061331 restraints weight = 7666.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.062006 restraints weight = 6338.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062528 restraints weight = 5750.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6279  Z= 0.101
  Angle     :  0.487  14.014   8773  Z= 0.243
  Chirality :  0.038   0.153   1011
  Planarity :  0.004   0.046    916
  Dihedral  : 18.709 123.160   1579
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.41 %
    Favored  : 90.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.85 (0.36), residues: 591
  helix:  2.02 (0.40), residues: 192
  sheet: -0.22 (0.47), residues: 112
  loop :  1.54 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 175 
 TYR   0.006   0.001   TYR A  52 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.001   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00229 /  0.10 ( 6279)
  covalent geometry    : angle       0.48688 /  0.24 ( 8773)
  hydrogen bonds       : bond        0.03533 /  2.35 (  235)
  hydrogen bonds       : angle       4.20535 /  2.92 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A  367 MET cc_start: 0.8492 (ttp) cc_final: 0.8203 (tmm)
REVERT: A  701 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8851 (mtp)
  outliers start: 5
  outliers final: 2
  residues processed: 39
  average time/residue: 0.0447
  time to fit residues: 2.6224
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 54 optimal weight:    9.9990
   chunk 4 optimal weight:    0.4980
   chunk 30 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 240 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.085282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.057631 restraints weight = 20367.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.059530 restraints weight = 10813.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.060821 restraints weight = 7691.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.061585 restraints weight = 6331.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061836 restraints weight = 5719.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6279  Z= 0.139
  Angle     :  0.527  15.396   8773  Z= 0.254
  Chirality :  0.038   0.133   1011
  Planarity :  0.004   0.046    916
  Dihedral  : 18.759 126.940   1579
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  9.35 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.82 (0.36), residues: 591
  helix:  2.03 (0.40), residues: 192
  sheet: -0.23 (0.47), residues: 112
  loop :  1.49 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 315 
 TYR   0.006   0.001   TYR A  51 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.14 ( 6279)
  covalent geometry    : angle       0.52701 /  0.25 ( 8773)
  hydrogen bonds       : bond        0.03579 /  2.40 (  235)
  hydrogen bonds       : angle       4.13058 /  2.89 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.122 
Fit side-chains
REVERT: A   86 HIS cc_start: 0.7947 (m90) cc_final: 0.7406 (m90)
REVERT: A  367 MET cc_start: 0.8516 (ttp) cc_final: 0.8245 (tmm)
REVERT: A  701 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.9017 (mtp)
  outliers start: 6
  outliers final: 2
  residues processed: 37
  average time/residue: 0.0545
  time to fit residues: 2.9170
Evaluate side-chains
  34 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 31
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 62 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 18 optimal weight:    2.9990
   chunk 59 optimal weight:   30.0000
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    0.6980
   chunk 22 optimal weight:    0.3980
   chunk 7 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.086067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.058629 restraints weight = 20478.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.060585 restraints weight = 10758.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.061740 restraints weight = 7630.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.062572 restraints weight = 6398.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.062802 restraints weight = 5757.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6279  Z= 0.092
  Angle     :  0.514  14.301   8773  Z= 0.246
  Chirality :  0.037   0.160   1011
  Planarity :  0.004   0.046    916
  Dihedral  : 18.760 126.349   1579
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.72 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.84 (0.36), residues: 591
  helix:  2.08 (0.40), residues: 192
  sheet: -0.18 (0.47), residues: 112
  loop :  1.46 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 545 
 TYR   0.007   0.001   TYR A  52 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.001   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.09 ( 6279)
  covalent geometry    : angle       0.51395 /  0.25 ( 8773)
  hydrogen bonds       : bond        0.03258 /  2.20 (  235)
  hydrogen bonds       : angle       3.97027 /  2.75 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 33
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   86 HIS cc_start: 0.7925 (m90) cc_final: 0.7428 (m90)
REVERT: A  367 MET cc_start: 0.8470 (ttp) cc_final: 0.8212 (tmm)
REVERT: A  701 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.8903 (mtp)
REVERT: A  702 MET cc_start: 0.8660 (mmm) cc_final: 0.8326 (mmm)
  outliers start: 5
  outliers final: 3
  residues processed: 37
  average time/residue: 0.0529
  time to fit residues: 2.9036
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0970
   chunk 4 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.3651 r_free = 0.3651 target = 0.085029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.057393 restraints weight = 20623.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.059279 restraints weight = 10933.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.060565 restraints weight = 7793.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.061189 restraints weight = 6478.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061661 restraints weight = 5891.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6279  Z= 0.121
  Angle     :  0.531  15.041   8773  Z= 0.251
  Chirality :  0.038   0.146   1011
  Planarity :  0.004   0.045    916
  Dihedral  : 18.728 125.148   1579
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.72 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.87 (0.36), residues: 591
  helix:  2.09 (0.40), residues: 192
  sheet: -0.12 (0.48), residues: 112
  loop :  1.46 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 301 
 TYR   0.006   0.001   TYR A  52 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.008   0.001   TRP A 435 
 HIS   0.003   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 6279)
  covalent geometry    : angle       0.53105 /  0.25 ( 8773)
  hydrogen bonds       : bond        0.03372 /  2.28 (  235)
  hydrogen bonds       : angle       3.94351 /  2.73 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A   86 HIS cc_start: 0.8011 (m90) cc_final: 0.7523 (m90)
REVERT: A  367 MET cc_start: 0.8471 (ttp) cc_final: 0.8200 (tmm)
REVERT: A  701 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8993 (mtp)
  outliers start: 5
  outliers final: 3
  residues processed: 36
  average time/residue: 0.0666
  time to fit residues: 3.4818
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:   40.0000
   chunk 40 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 46 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.9320

-------------------------------------------------------------------------------
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 = 0.3656 r_free = 0.3656 target = 0.085232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.057721 restraints weight = 20608.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059615 restraints weight = 10881.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.060929 restraints weight = 7743.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.061718 restraints weight = 6407.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061916 restraints weight = 5776.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.2948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6279  Z= 0.103
  Angle     :  0.538  14.857   8773  Z= 0.252
  Chirality :  0.037   0.152   1011
  Planarity :  0.004   0.046    916
  Dihedral  : 18.690 125.086   1579
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.47 %
    Favored  : 88.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.87 (0.36), residues: 591
  helix:  2.05 (0.40), residues: 193
  sheet: -0.08 (0.47), residues: 112
  loop :  1.49 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 315 
 TYR   0.006   0.001   TYR A 318 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.009   0.001   TRP A 435 
 HIS   0.002   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.10 ( 6279)
  covalent geometry    : angle       0.53787 /  0.25 ( 8773)
  hydrogen bonds       : bond        0.03217 /  2.18 (  235)
  hydrogen bonds       : angle       3.87464 /  2.67 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A   86 HIS cc_start: 0.7995 (m90) cc_final: 0.7539 (m90)
REVERT: A  367 MET cc_start: 0.8443 (ttp) cc_final: 0.8201 (tmm)
REVERT: A  701 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8982 (mtp)
  outliers start: 4
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0539
  time to fit residues: 2.6781
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 57 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 53 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.084122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.056507 restraints weight = 20698.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.058357 restraints weight = 11046.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.059612 restraints weight = 7926.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.060227 restraints weight = 6590.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.060718 restraints weight = 5992.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6279  Z= 0.150
  Angle     :  0.567  15.292   8773  Z= 0.266
  Chirality :  0.038   0.152   1011
  Planarity :  0.004   0.045    916
  Dihedral  : 18.658 124.569   1579
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 10.47 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.88 (0.37), residues: 591
  helix:  1.99 (0.40), residues: 193
  sheet: -0.06 (0.47), residues: 112
  loop :  1.52 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 545 
 TYR   0.007   0.001   TYR A 661 
 PHE   0.010   0.001   PHE A  48 
 TRP   0.007   0.001   TRP A 287 
 HIS   0.004   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 ( 6279)
  covalent geometry    : angle       0.56720 /  0.27 ( 8773)
  hydrogen bonds       : bond        0.03673 /  2.48 (  235)
  hydrogen bonds       : angle       3.98996 /  2.76 (  597)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 31
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A  367 MET cc_start: 0.8494 (ttp) cc_final: 0.8230 (tmm)
REVERT: A  701 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8932 (mtp)
  outliers start: 5
  outliers final: 3
  residues processed: 34
  average time/residue: 0.0565
  time to fit residues: 2.8010
Evaluate side-chains
  35 residues out of total 535 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  277 MET
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  701 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:   20.0000
   chunk 31 optimal weight:    0.4980
   chunk 62 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.084537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.056952 restraints weight = 20537.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.058900 restraints weight = 10947.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.060084 restraints weight = 7815.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060858 restraints weight = 6551.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.061264 restraints weight = 5943.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6279  Z= 0.111
  Angle     :  0.533  15.366   8773  Z= 0.250
  Chirality :  0.037   0.152   1011
  Planarity :  0.004   0.046    916
  Dihedral  : 18.598 124.275   1579
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 10.28 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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:  1.94 (0.37), residues: 591
  helix:  2.07 (0.40), residues: 193
  sheet: -0.03 (0.47), residues: 112
  loop :  1.55 (0.40), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 545 
 TYR   0.006   0.001   TYR A 318 
 PHE   0.012   0.001   PHE A  48 
 TRP   0.010   0.001   TRP A 435 
 HIS   0.002   0.000   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 6279)
  covalent geometry    : angle       0.53312 /  0.25 ( 8773)
  hydrogen bonds       : bond        0.03290 /  2.23 (  235)
  hydrogen bonds       : angle       3.88263 /  2.67 (  597)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 903.29 seconds
wall clock time: 16 minutes 17.70 seconds (977.70 seconds total)