Starting phenix.real_space_refine
on Sat Aug 23 01:18:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iss_35694/08_2025/8iss_35694.map"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.149
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      79      5.49       5
     Mg      1      5.21       5
     S      27      5.16       5
     C    5310      2.51       5
     N    1557      2.21       5
     O    1833      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8807
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 941
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
    Chain: "B"
      Number of atoms: 1839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1839
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 10, 'TRANS': 212}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2018
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 2018
          Classifications: {'peptide': 257}
          Link IDs: {'PTRANS': 18, 'TRANS': 238}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2298
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 21, 'TRANS': 267}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 1710
          Inner-chain residues flagged as termini: ['pdbres="  A E  47 "']
          Classifications: {'RNA': 80}
          Modifications used: {'5*END': 1, 'p5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 29}
          Link IDs: {'rna2p': 18, 'rna3p': 61}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.45, per 1000 atoms: 0.28
  Number of scatterers: 8807
  At special positions: 0
  Unit cell: (74.905, 86.51, 131.875, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      27     16.00
     P      79     15.00
     Mg      1     11.99
     O    1833      8.00
     N    1557      7.00
     C    5310      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: 1.00
  Conformation dependent library (CDL) restraints added in 296.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1668

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      37.3% alpha, 17.3% beta
      28 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 51
    Processing helix  chain 'A' and resid 56 through 73
    Processing helix  chain 'A' and resid 85 through 88
    Processing helix  chain 'A' and resid 115 through 130
    Processing helix  chain 'B' and resid 53 through 63
    Processing helix  chain 'B' and resid 300 through 310
    Processing helix  chain 'B' and resid 324 through 336
    Processing helix  chain 'B' and resid 339 through 351
    Processing helix  chain 'B' and resid 400 through 414
    Processing helix  chain 'B' and resid 432 through 442
      Proline residue:  B 437  - end of helix
    Processing helix  chain 'B' and resid 456 through 460
      removed outlier: 3.609A  pdb=" N   ARG B 459 " --> pdb=" O   SER B 456 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   SER B 460 " --> pdb=" O   ARG B 457 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 456 through 460'
    Processing helix  chain 'C' and resid 15 through 25
    Processing helix  chain 'C' and resid 53 through 63
      removed outlier: 3.667A  pdb=" N   LEU C  60 " --> pdb=" O   GLU C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 112
    Processing helix  chain 'C' and resid 114 through 126
      removed outlier: 3.599A  pdb=" N   LYS C 126 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 230
      removed outlier: 3.707A  pdb=" N   ARG C 220 " --> pdb=" O   ALA C 216 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG C 230 " --> pdb=" O   ASP C 226 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 284
    Processing helix  chain 'D' and resid 19 through 28
    Processing helix  chain 'D' and resid 48 through 67
    Processing helix  chain 'D' and resid 96 through 101
    Processing helix  chain 'D' and resid 113 through 123
    Processing helix  chain 'D' and resid 136 through 145
    Processing helix  chain 'D' and resid 151 through 164
      removed outlier: 3.550A  pdb=" N   TYR D 155 " --> pdb=" O   THR D 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 410 through 414
      removed outlier: 3.801A  pdb=" N   ALA D 414 " --> pdb=" O   PRO D 411 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 424
    Processing helix  chain 'D' and resid 454 through 459
      removed outlier: 3.865A  pdb=" N   ALA D 459 " --> pdb=" O   ASP D 456 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 484 through 496
    Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 84
      removed outlier: 3.734A  pdb=" N   GLU A  78 " --> pdb=" O   THR A  95 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   CYS A  91 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 108 through 109
      removed outlier: 6.671A  pdb=" N   THR A 108 " --> pdb=" O   VAL A 144 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139
      removed outlier: 3.918A  pdb=" N   LYS C 298 " --> pdb=" O   GLN C 294 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   ILE C 259 " --> pdb=" O   LEU C 289 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   CYS C 291 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   GLN C 261 " --> pdb=" O   CYS C 291 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   TYR C 258 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   PHE C 244 " --> pdb=" O   ALA C 260 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   CYS C 262 " --> pdb=" O   GLY C 242 " (cutoff:3.500A)
      removed outlier: 9.893A  pdb=" N   GLY C 242 " --> pdb=" O   CYS C 262 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ALA C 237 " --> pdb=" O   GLY C 242 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   PHE C 244 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   SER C 235 " --> pdb=" O   PHE C 244 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL C 246 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   PHE C 233 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 50
    Processing sheet with id=AA5, first strand: chain 'B' and resid 366 through 368
      removed outlier: 4.114A  pdb=" N   TYR B 380 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU B 418 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   LEU D 504 " --> pdb=" O   SER D 511 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   PHE D 515 " --> pdb=" O   LEU D 500 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   LEU D 500 " --> pdb=" O   PHE D 515 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ALA D 471 " --> pdb=" O   ASP D 451 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   ASP D 451 " --> pdb=" O   ALA D 471 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   MET D 473 " --> pdb=" O   ILE D 449 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 386 through 388
      removed outlier: 4.066A  pdb=" N   LEU B 418 " --> pdb=" O   LEU B 450 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 50 through 52
      removed outlier: 4.195A  pdb=" N   SER C  11 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU C  12 " --> pdb=" O   GLU C   5 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLU C   5 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   VAL C   4 " --> pdb=" O   THR C  67 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 187
      removed outlier: 4.395A  pdb=" N   ARG D  70 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 195 through 197
      removed outlier: 3.566A  pdb=" N   VAL C 195 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 104 through 106
      removed outlier: 5.010A  pdb=" N   GLN D 110 " --> pdb=" O   LEU D  91 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL D  78 " --> pdb=" O   HIS D 127 " (cutoff:3.500A)

    314 hydrogen bonds defined for protein.
    861 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      71 hydrogen bonds
      118 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.26 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: 2461
        1.34 -     1.45: 1946
        1.45 -     1.57: 4569
        1.57 -     1.69: 157
        1.69 -     1.81: 43
  Bond restraints: 9176
  Sorted by residual:
  bond pdb=" C   ASP A 132 "
       pdb=" N   PRO A 133 "
    ideal  model  delta    sigma   weight residual
    1.326  1.339 -0.013 1.44e-02 4.82e+03 7.58e-01
  bond pdb=" C   ALA B   8 "
       pdb=" N   PRO B   9 "
    ideal  model  delta    sigma   weight residual
    1.335  1.342 -0.007 8.70e-03 1.32e+04 7.27e-01
  bond pdb=" CG  LYS B 330 "
       pdb=" CD  LYS B 330 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.02e-01
  bond pdb=" CB  LYS B 330 "
       pdb=" CG  LYS B 330 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.83e-01
  bond pdb=" CD  LYS B 330 "
       pdb=" CE  LYS B 330 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.54e-01
  ... (remaining 9171 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 12709
        2.28 -     4.56: 100
        4.56 -     6.84: 4
        6.84 -     9.12: 1
        9.12 -    11.40: 1
  Bond angle restraints: 12815
  Sorted by residual:
  angle pdb=" CG  LYS D  32 "
        pdb=" CD  LYS D  32 "
        pdb=" CE  LYS D  32 "
      ideal   model   delta    sigma   weight residual
     111.30  122.70  -11.40 2.30e+00 1.89e-01 2.46e+01
  angle pdb=" CB  LYS B 330 "
        pdb=" CG  LYS B 330 "
        pdb=" CD  LYS B 330 "
      ideal   model   delta    sigma   weight residual
     111.30  118.42   -7.12 2.30e+00 1.89e-01 9.60e+00
  angle pdb=" C   LEU C 113 "
        pdb=" N   GLU C 114 "
        pdb=" CA  GLU C 114 "
      ideal   model   delta    sigma   weight residual
     121.54  126.48   -4.94 1.91e+00 2.74e-01 6.69e+00
  angle pdb=" CA  TYR B 343 "
        pdb=" CB  TYR B 343 "
        pdb=" CG  TYR B 343 "
      ideal   model   delta    sigma   weight residual
     113.90  109.49    4.41 1.80e+00 3.09e-01 6.02e+00
  angle pdb=" C   TYR B 318 "
        pdb=" N   GLU B 319 "
        pdb=" CA  GLU B 319 "
      ideal   model   delta    sigma   weight residual
     121.54  125.89   -4.35 1.91e+00 2.74e-01 5.19e+00
  ... (remaining 12810 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.10: 4706
       19.10 -    38.19: 616
       38.19 -    57.29: 207
       57.29 -    76.38: 103
       76.38 -    95.48: 14
  Dihedral angle restraints: 5646
    sinusoidal: 3065
      harmonic: 2581
  Sorted by residual:
  dihedral pdb=" CA  LYS B 320 "
           pdb=" C   LYS B 320 "
           pdb=" N   GLU B 321 "
           pdb=" CA  GLU B 321 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.46  -23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  ILE D 510 "
           pdb=" C   ILE D 510 "
           pdb=" N   SER D 511 "
           pdb=" CA  SER D 511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.94  -20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  PHE D 502 "
           pdb=" C   PHE D 502 "
           pdb=" N   ALA D 503 "
           pdb=" CA  ALA D 503 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.85  -18.15     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1016
       0.028 -    0.057: 320
       0.057 -    0.085: 66
       0.085 -    0.113: 58
       0.113 -    0.142: 18
  Chirality restraints: 1478
  Sorted by residual:
  chirality pdb=" CA  VAL B 355 "
            pdb=" N   VAL B 355 "
            pdb=" C   VAL B 355 "
            pdb=" CB  VAL B 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality pdb=" CA  VAL D 482 "
            pdb=" N   VAL D 482 "
            pdb=" C   VAL D 482 "
            pdb=" CB  VAL D 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.59e-01
  chirality pdb=" CA  ILE C 259 "
            pdb=" N   ILE C 259 "
            pdb=" C   ILE C 259 "
            pdb=" CB  ILE C 259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  ... (remaining 1475 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 114 "    0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLU C 114 "   -0.061 2.00e-02 2.50e+03
        pdb=" O   GLU C 114 "    0.023 2.00e-02 2.50e+03
        pdb=" N   LYS C 115 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY D  39 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO D  40 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO D  40 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D  40 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 372 "    0.024 5.00e-02 4.00e+02   3.56e-02 2.03e+00
        pdb=" N   PRO B 373 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 373 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 373 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 138
        2.60 -     3.18: 7492
        3.18 -     3.75: 14396
        3.75 -     4.33: 19760
        4.33 -     4.90: 32234
  Nonbonded interactions: 74020
  Sorted by model distance:
  nonbonded pdb=" O2'   G E  50 "
            pdb=" OP2   U E  54 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" O   GLY A 158 "
            pdb=" OG  SER C 303 "
     model   vdw
     2.042 3.040
  nonbonded pdb=" OP2   G E  12 "
            pdb="MG    MG E 101 "
     model   vdw
     2.051 2.170
  nonbonded pdb=" O2'   C E  35 "
            pdb=" O3'   G E  38 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" O2'   C E  35 "
            pdb=" O2'   G E  38 "
     model   vdw
     2.091 3.040
  ... (remaining 74015 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:             0.660
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.700
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
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      :  0.003   0.027   9176  Z= 0.116
  Angle     :  0.514  11.398  12815  Z= 0.264
  Chirality :  0.036   0.142   1478
  Planarity :  0.004   0.044   1344
  Dihedral  : 20.029  95.477   3978
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 22.51 %
    Favored  : 77.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.16 (0.29), residues: 873
  helix:  0.81 (0.30), residues: 316
  sheet: -2.26 (0.40), residues: 165
  loop : -1.34 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  10 
 TYR   0.017   0.001   TYR D 155 
 PHE   0.010   0.001   PHE D 512 
 TRP   0.014   0.001   TRP D  99 
 HIS   0.003   0.001   HIS C 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9176)
  covalent geometry    : angle       0.51437 (12815)
  hydrogen bonds       : bond        0.15745 (  378)
  hydrogen bonds       : angle       6.94196 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.300 
Fit side-chains
REVERT: B   11 ARG cc_start: 0.6382 (ttm110) cc_final: 0.5869 (mtp85)
  outliers start: 3
  outliers final: 3
  residues processed: 102
  average time/residue: 0.1409
  time to fit residues: 18.5479
Evaluate side-chains
  93 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  478 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0040
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4950

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

Flipped N/Q/H residues before XYZ refinement:
C 120 GLN
C 211 HIS
D 507 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.181177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.145509 restraints weight = 9801.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 1.95
r_work: 0.3364 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9176  Z= 0.118
  Angle     :  0.544   6.311  12815  Z= 0.277
  Chirality :  0.038   0.198   1478
  Planarity :  0.004   0.044   1344
  Dihedral  : 18.467  91.410   2233
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.47 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.30), residues: 873
  helix:  1.39 (0.31), residues: 300
  sheet: -1.87 (0.42), residues: 157
  loop : -0.95 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  10 
 TYR   0.016   0.002   TYR B 343 
 PHE   0.013   0.001   PHE A 139 
 TRP   0.015   0.001   TRP D  99 
 HIS   0.004   0.001   HIS C 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 9176)
  covalent geometry    : angle       0.54417 (12815)
  hydrogen bonds       : bond        0.04366 (  378)
  hydrogen bonds       : angle       4.91239 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.6008 (mm) cc_final: 0.5806 (mm)
REVERT: A   49 MET cc_start: 0.5821 (mpp) cc_final: 0.5347 (mpp)
REVERT: A   71 MET cc_start: 0.6138 (mmm) cc_final: 0.5389 (mmm)
REVERT: A  145 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7559 (mp0)
REVERT: B   11 ARG cc_start: 0.6091 (ttm110) cc_final: 0.5528 (mtp85)
REVERT: B  380 TYR cc_start: 0.6772 (m-80) cc_final: 0.6511 (m-80)
REVERT: C   45 ARG cc_start: 0.7827 (ttt180) cc_final: 0.7525 (mtt-85)
REVERT: C  103 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5080 (mp0)
REVERT: C  272 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.6966 (mt0)
REVERT: D   22 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7690 (mt-10)
REVERT: D   85 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6392 (pm20)
REVERT: D  497 ASP cc_start: 0.7652 (m-30) cc_final: 0.7422 (t0)
  outliers start: 23
  outliers final: 5
  residues processed: 125
  average time/residue: 0.1234
  time to fit residues: 20.4770
Evaluate side-chains
  95 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain D residue   30 SER
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  478 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 14 optimal weight:   10.0000
   chunk 81 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B  48 ASN
D 403 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.178519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.142547 restraints weight = 9754.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.96
r_work: 0.3325 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9176  Z= 0.141
  Angle     :  0.536   6.294  12815  Z= 0.272
  Chirality :  0.038   0.145   1478
  Planarity :  0.004   0.046   1344
  Dihedral  : 18.296  90.516   2232
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.73 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.30), residues: 873
  helix:  1.32 (0.31), residues: 307
  sheet: -1.60 (0.41), residues: 164
  loop : -0.87 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  10 
 TYR   0.017   0.002   TYR B 343 
 PHE   0.014   0.001   PHE A 139 
 TRP   0.012   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9176)
  covalent geometry    : angle       0.53599 (12815)
  hydrogen bonds       : bond        0.04279 (  378)
  hydrogen bonds       : angle       4.56867 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.5816 (mm) cc_final: 0.5451 (mm)
REVERT: A   71 MET cc_start: 0.6105 (mmm) cc_final: 0.5411 (mmm)
REVERT: A  145 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7574 (mp0)
REVERT: B   41 ARG cc_start: 0.7626 (mtp85) cc_final: 0.7380 (mtp85)
REVERT: C  272 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6937 (mm-40)
REVERT: D   22 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7648 (mt-10)
REVERT: D   85 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6535 (pm20)
  outliers start: 26
  outliers final: 12
  residues processed: 116
  average time/residue: 0.1220
  time to fit residues: 18.7256
Evaluate side-chains
  104 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue   95 THR
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.9724

-------------------------------------------------------------------------------
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 = 0.4004 r_free = 0.4004 target = 0.175718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.139494 restraints weight = 9831.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.96
r_work: 0.3469 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9176  Z= 0.131
  Angle     :  0.522   7.957  12815  Z= 0.264
  Chirality :  0.038   0.152   1478
  Planarity :  0.004   0.046   1344
  Dihedral  : 18.344  91.800   2232
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.25 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.30), residues: 873
  helix:  1.38 (0.30), residues: 307
  sheet: -1.66 (0.42), residues: 163
  loop : -0.78 (0.32), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  10 
 TYR   0.016   0.002   TYR B 343 
 PHE   0.014   0.001   PHE A 139 
 TRP   0.011   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 9176)
  covalent geometry    : angle       0.52198 (12815)
  hydrogen bonds       : bond        0.04162 (  378)
  hydrogen bonds       : angle       4.37712 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5672 (mm)
REVERT: A   71 MET cc_start: 0.6068 (mmm) cc_final: 0.5420 (mmm)
REVERT: A  145 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7559 (mp0)
REVERT: B   41 ARG cc_start: 0.7731 (mtp85) cc_final: 0.7453 (mtp85)
REVERT: B  380 TYR cc_start: 0.6854 (m-80) cc_final: 0.6528 (m-80)
REVERT: B  435 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6177 (mp0)
REVERT: C  272 GLN cc_start: 0.7496 (OUTLIER) cc_final: 0.6964 (mm-40)
REVERT: D   85 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6659 (pm20)
REVERT: D  172 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6797 (tt0)
  outliers start: 28
  outliers final: 15
  residues processed: 118
  average time/residue: 0.1192
  time to fit residues: 18.8878
Evaluate side-chains
  112 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0470
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7478

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.177626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.141176 restraints weight = 9821.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3602 rms_B_bonded: 1.99
r_work: 0.3465 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3313 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9176  Z= 0.115
  Angle     :  0.506   7.404  12815  Z= 0.255
  Chirality :  0.037   0.141   1478
  Planarity :  0.004   0.046   1344
  Dihedral  : 18.342  92.501   2232
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 23.17 %
    Favored  : 73.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.30), residues: 873
  helix:  1.45 (0.30), residues: 308
  sheet: -1.52 (0.42), residues: 161
  loop : -0.61 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG C  10 
 TYR   0.016   0.002   TYR D 119 
 PHE   0.013   0.001   PHE A 139 
 TRP   0.010   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9176)
  covalent geometry    : angle       0.50555 (12815)
  hydrogen bonds       : bond        0.03988 (  378)
  hydrogen bonds       : angle       4.26452 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.5895 (OUTLIER) cc_final: 0.5539 (mm)
REVERT: A   71 MET cc_start: 0.5839 (mmm) cc_final: 0.5214 (mmm)
REVERT: A  145 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7610 (mp0)
REVERT: B  380 TYR cc_start: 0.6841 (m-80) cc_final: 0.6558 (m-80)
REVERT: B  435 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6147 (mp0)
REVERT: C  272 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6928 (mm-40)
REVERT: D   85 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6664 (pm20)
REVERT: D  172 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6921 (tt0)
  outliers start: 27
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0964
  time to fit residues: 16.0269
Evaluate side-chains
  111 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   70 ILE
Chi-restraints excluded: chain B residue  324 THR
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  185 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain C residue  272 GLN
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0060
   chunk 12 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0020
   chunk 87 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.9006

-------------------------------------------------------------------------------
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 = 0.4053 r_free = 0.4053 target = 0.180062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.144266 restraints weight = 9800.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 1.97
r_work: 0.3482 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3330 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.2224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9176  Z= 0.124
  Angle     :  0.508   7.532  12815  Z= 0.256
  Chirality :  0.037   0.142   1478
  Planarity :  0.004   0.053   1344
  Dihedral  : 18.339  92.013   2232
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 23.43 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.30), residues: 873
  helix:  1.48 (0.30), residues: 308
  sheet: -1.42 (0.44), residues: 159
  loop : -0.55 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  10 
 TYR   0.021   0.002   TYR B 343 
 PHE   0.012   0.001   PHE A 139 
 TRP   0.010   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9176)
  covalent geometry    : angle       0.50801 (12815)
  hydrogen bonds       : bond        0.04058 (  378)
  hydrogen bonds       : angle       4.21973 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 91
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.5772 (OUTLIER) cc_final: 0.5422 (mm)
REVERT: A   71 MET cc_start: 0.5838 (mmm) cc_final: 0.5218 (mmm)
REVERT: A  145 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7611 (mp0)
REVERT: B  380 TYR cc_start: 0.6650 (m-80) cc_final: 0.6425 (m-80)
REVERT: B  435 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6232 (mp0)
REVERT: C   45 ARG cc_start: 0.7936 (ttt180) cc_final: 0.7427 (mtp85)
REVERT: D   85 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6685 (pm20)
REVERT: D  172 GLN cc_start: 0.7498 (mm-40) cc_final: 0.7043 (tt0)
  outliers start: 29
  outliers final: 16
  residues processed: 115
  average time/residue: 0.0833
  time to fit residues: 13.1509
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 42 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  48 ASN
C  43 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.173573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.137128 restraints weight = 9950.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.98
r_work: 0.3352 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9176  Z= 0.226
  Angle     :  0.602   8.485  12815  Z= 0.303
  Chirality :  0.041   0.172   1478
  Planarity :  0.005   0.047   1344
  Dihedral  : 18.442  89.787   2232
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.43 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.30), residues: 873
  helix:  1.15 (0.30), residues: 309
  sheet: -1.52 (0.42), residues: 168
  loop : -0.57 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C  10 
 TYR   0.026   0.003   TYR B 343 
 PHE   0.015   0.002   PHE B   6 
 TRP   0.012   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 9176)
  covalent geometry    : angle       0.60158 (12815)
  hydrogen bonds       : bond        0.04807 (  378)
  hydrogen bonds       : angle       4.44267 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5509 (mm)
REVERT: A   49 MET cc_start: 0.5277 (mmm) cc_final: 0.5059 (mmt)
REVERT: A   71 MET cc_start: 0.6090 (mmm) cc_final: 0.5412 (mmm)
REVERT: A  145 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7731 (mp0)
REVERT: B  380 TYR cc_start: 0.6878 (m-80) cc_final: 0.6616 (m-80)
REVERT: B  390 HIS cc_start: 0.7401 (m90) cc_final: 0.6974 (m170)
REVERT: B  435 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6175 (mp0)
REVERT: C   45 ARG cc_start: 0.8011 (ttt180) cc_final: 0.7524 (mtp85)
REVERT: D   85 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6618 (pm20)
  outliers start: 31
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1027
  time to fit residues: 16.4200
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain B residue  454 VAL
Chi-restraints excluded: chain C residue   66 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  427 LEU
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 88 optimal weight:    7.9990
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0070
   overall best weight:    0.7402

-------------------------------------------------------------------------------
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 = 0.4047 r_free = 0.4047 target = 0.179438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.143656 restraints weight = 9854.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 1.97
r_work: 0.3476 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9176  Z= 0.119
  Angle     :  0.519   8.218  12815  Z= 0.262
  Chirality :  0.037   0.155   1478
  Planarity :  0.004   0.042   1344
  Dihedral  : 18.424  93.410   2232
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 25.52 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.08 (0.30), residues: 873
  helix:  1.40 (0.30), residues: 310
  sheet: -1.44 (0.43), residues: 157
  loop : -0.54 (0.32), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  10 
 TYR   0.029   0.002   TYR D 119 
 PHE   0.014   0.001   PHE A 139 
 TRP   0.009   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9176)
  covalent geometry    : angle       0.51877 (12815)
  hydrogen bonds       : bond        0.04093 (  378)
  hydrogen bonds       : angle       4.25924 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5438 (mm)
REVERT: A   71 MET cc_start: 0.5897 (mmm) cc_final: 0.5290 (mmm)
REVERT: A  145 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7658 (mp0)
REVERT: B   11 ARG cc_start: 0.5965 (ttm110) cc_final: 0.5571 (tpp-160)
REVERT: B  380 TYR cc_start: 0.6740 (m-80) cc_final: 0.6500 (m-80)
REVERT: B  390 HIS cc_start: 0.7370 (m90) cc_final: 0.6967 (m170)
REVERT: B  396 ARG cc_start: 0.7934 (ttt-90) cc_final: 0.7663 (ttp80)
REVERT: B  435 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6245 (mp0)
REVERT: C   53 MET cc_start: 0.7797 (mtt) cc_final: 0.7548 (mtm)
REVERT: D   21 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7295 (ttm-80)
REVERT: D   85 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6607 (pm20)
REVERT: D  172 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7113 (tt0)
  outliers start: 20
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0787
  time to fit residues: 11.4021
Evaluate side-chains
  101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  138 SER
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain C residue  268 THR
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0010
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0670
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.8980
   chunk 87 optimal weight:    9.9990
   chunk 63 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.5124

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.191668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.155790 restraints weight = 9991.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3884 rms_B_bonded: 1.89
r_work: 0.3692 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9176  Z= 0.103
  Angle     :  0.500   7.970  12815  Z= 0.252
  Chirality :  0.037   0.151   1478
  Planarity :  0.004   0.044   1344
  Dihedral  : 18.371  93.774   2232
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 25.00 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.30), residues: 873
  helix:  1.60 (0.30), residues: 309
  sheet: -1.39 (0.44), residues: 155
  loop : -0.45 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C  10 
 TYR   0.023   0.002   TYR D 119 
 PHE   0.013   0.001   PHE A 139 
 TRP   0.008   0.001   TRP D  82 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 9176)
  covalent geometry    : angle       0.49956 (12815)
  hydrogen bonds       : bond        0.03939 (  378)
  hydrogen bonds       : angle       4.13708 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.6138 (OUTLIER) cc_final: 0.5747 (mm)
REVERT: A   71 MET cc_start: 0.5979 (mmm) cc_final: 0.5557 (mmm)
REVERT: A  145 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7671 (mp0)
REVERT: B   11 ARG cc_start: 0.6222 (ttm110) cc_final: 0.5855 (tpp-160)
REVERT: B  380 TYR cc_start: 0.6608 (m-80) cc_final: 0.6403 (m-80)
REVERT: B  435 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.6388 (mp0)
REVERT: D   21 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7523 (ttm-80)
REVERT: D   85 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6875 (pm20)
  outliers start: 19
  outliers final: 12
  residues processed: 100
  average time/residue: 0.0815
  time to fit residues: 11.4000
Evaluate side-chains
  96 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    8.9990
   chunk 46 optimal weight:    8.9990
   chunk 28 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.190637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155076 restraints weight = 9998.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 1.85
r_work: 0.3686 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3548 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9176  Z= 0.125
  Angle     :  0.517   7.486  12815  Z= 0.260
  Chirality :  0.037   0.133   1478
  Planarity :  0.004   0.058   1344
  Dihedral  : 18.356  92.379   2232
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 25.39 %
    Favored  : 72.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 873
  helix:  1.56 (0.30), residues: 309
  sheet: -1.42 (0.43), residues: 160
  loop : -0.37 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C  10 
 TYR   0.022   0.002   TYR D 119 
 PHE   0.013   0.001   PHE A 139 
 TRP   0.010   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9176)
  covalent geometry    : angle       0.51701 (12815)
  hydrogen bonds       : bond        0.04074 (  378)
  hydrogen bonds       : angle       4.18756 (  979)

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

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

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1746 Ramachandran restraints generated.
    873 Oldfield, 0 Emsley, 873 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 LEU cc_start: 0.6158 (OUTLIER) cc_final: 0.5744 (mm)
REVERT: A   71 MET cc_start: 0.6180 (mmm) cc_final: 0.5696 (mmm)
REVERT: A  145 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7856 (mp0)
REVERT: B   11 ARG cc_start: 0.6274 (ttm110) cc_final: 0.5901 (tpp-160)
REVERT: B  380 TYR cc_start: 0.6914 (m-80) cc_final: 0.6665 (m-80)
REVERT: B  390 HIS cc_start: 0.7489 (m90) cc_final: 0.7094 (m170)
REVERT: B  435 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.6526 (mp0)
REVERT: D   85 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6906 (pm20)
  outliers start: 16
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0866
  time to fit residues: 11.8983
Evaluate side-chains
  96 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain B residue  435 GLU
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  226 ASP
Chi-restraints excluded: chain D residue   74 LEU
Chi-restraints excluded: chain D residue   85 GLU
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain D residue  101 THR
Chi-restraints excluded: chain D residue  151 THR
Chi-restraints excluded: chain D residue  168 VAL
Chi-restraints excluded: chain D residue  413 GLN
Chi-restraints excluded: chain D residue  478 PHE
Chi-restraints excluded: chain D residue  486 CYS
Chi-restraints excluded: chain D residue  523 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  48 ASN
B 336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.190191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.154427 restraints weight = 9876.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 1.85
r_work: 0.3671 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9176  Z= 0.124
  Angle     :  0.515   7.517  12815  Z= 0.259
  Chirality :  0.037   0.135   1478
  Planarity :  0.004   0.059   1344
  Dihedral  : 18.359  92.443   2232
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 25.52 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.30), residues: 873
  helix:  1.61 (0.30), residues: 309
  sheet: -1.40 (0.44), residues: 160
  loop : -0.36 (0.32), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG C  10 
 TYR   0.023   0.002   TYR D 119 
 PHE   0.013   0.001   PHE A 139 
 TRP   0.010   0.001   TRP D  82 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9176)
  covalent geometry    : angle       0.51534 (12815)
  hydrogen bonds       : bond        0.04099 (  378)
  hydrogen bonds       : angle       4.17834 (  979)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2128.58 seconds
wall clock time: 37 minutes 15.52 seconds (2235.52 seconds total)