Starting phenix.real_space_refine
on Tue Mar  3 17:14:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u1t_26305/03_2026/7u1t_26305_neut.cif"
  }
  resolution = 3.3
  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=   0.001
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     118      5.49       5
     S      32      5.16       5
     C    4440      2.51       5
     N    1364      2.21       5
     O    1620      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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7574
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1336
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 18, 'TRANS': 157}
    Chain: "B"
      Number of atoms: 1245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1245
          Classifications: {'peptide': 162}
          Link IDs: {'PTRANS': 15, 'TRANS': 146}
    Chain: "C"
      Number of atoms: 1336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1336
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 18, 'TRANS': 157}
    Chain: "D"
      Number of atoms: 1238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1238
          Classifications: {'peptide': 161}
          Link IDs: {'PTRANS': 15, 'TRANS': 145}
    Chain: "E"
      Number of atoms: 1209
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1209
          Classifications: {'DNA': 59}
          Link IDs: {'rna3p': 58}
    Chain: "F"
      Number of atoms: 1210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 1210
          Classifications: {'DNA': 59}
          Link IDs: {'rna3p': 58}
  Time building chain proxies: 1.65, per 1000 atoms: 0.22
  Number of scatterers: 7574
  At special positions: 0
  Unit cell: (113.52, 131.58, 129, 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      32     16.00
     P     118     15.00
     O    1620      8.00
     N    1364      7.00
     C    4440      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: 0.77
  Conformation dependent library (CDL) restraints added in 196.7 milliseconds
  

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1174

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 6 sheets defined
      33.9% alpha, 27.0% beta
      54 base pairs and 89 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 475 through 492
      removed outlier: 3.693A  pdb=" N   SER A 492 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 528
    Processing helix  chain 'A' and resid 568 through 586
    Processing helix  chain 'A' and resid 587 through 592
    Processing helix  chain 'B' and resid 475 through 492
      removed outlier: 4.019A  pdb=" N   SER B 492 " --> pdb=" O   LEU B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 528
    Processing helix  chain 'B' and resid 568 through 586
    Processing helix  chain 'C' and resid 475 through 492
      removed outlier: 4.030A  pdb=" N   SER C 492 " --> pdb=" O   LEU C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 513 through 528
    Processing helix  chain 'C' and resid 568 through 586
      removed outlier: 3.515A  pdb=" N   ALA C 572 " --> pdb=" O   THR C 568 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL C 574 " --> pdb=" O   ILE C 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 588 through 593
    Processing helix  chain 'D' and resid 475 through 492
      removed outlier: 3.993A  pdb=" N   SER D 492 " --> pdb=" O   LEU D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 513 through 528
    Processing helix  chain 'D' and resid 568 through 586
    Processing helix  chain 'D' and resid 588 through 592
      removed outlier: 3.985A  pdb=" N   ASN D 592 " --> pdb=" O   ALA D 588 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 588 through 592'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 532 through 533
      removed outlier: 5.180A  pdb=" N   CYS A 560 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY A 511 " --> pdb=" O   CYS A 560 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL A 504 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   VAL A 595 " --> pdb=" O   GLY B 603 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   GLY B 603 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL A 597 " --> pdb=" O   ASP B 601 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASP B 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 599 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL B 597 " --> pdb=" O   ASP A 601 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   GLY A 603 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL B 595 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   VAL B 504 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 560 " --> pdb=" O   GLY B 511 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 538
      removed outlier: 5.180A  pdb=" N   CYS A 560 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY A 511 " --> pdb=" O   CYS A 560 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   VAL A 504 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
      removed outlier: 9.132A  pdb=" N   VAL A 595 " --> pdb=" O   GLY B 603 " (cutoff:3.500A)
      removed outlier: 8.185A  pdb=" N   GLY B 603 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   VAL A 597 " --> pdb=" O   ASP B 601 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   ASP B 601 " --> pdb=" O   VAL A 597 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A 599 " --> pdb=" O   SER B 599 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   VAL B 597 " --> pdb=" O   ASP A 601 " (cutoff:3.500A)
      removed outlier: 7.284A  pdb=" N   GLY A 603 " --> pdb=" O   VAL B 595 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL B 595 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   VAL B 504 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   CYS B 560 " --> pdb=" O   GLY B 511 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   VAL B 559 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 532 through 533
    Processing sheet with id=AA4, first strand: chain 'C' and resid 532 through 533
      removed outlier: 5.102A  pdb=" N   VAL C 504 " --> pdb=" O   PHE C 600 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 532 through 533
      removed outlier: 5.259A  pdb=" N   VAL D 559 " --> pdb=" O   LEU D 539 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 532 through 533
      removed outlier: 5.089A  pdb=" N   CYS D 560 " --> pdb=" O   GLY D 511 " (cutoff:3.500A)

    269 hydrogen bonds defined for protein.
    762 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      126 hydrogen bonds
      252 hydrogen bond angles
      0 basepair planarities
      54 basepair parallelities
      89 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1312
        1.33 -     1.45: 2523
        1.45 -     1.57: 3898
        1.57 -     1.69: 234
        1.69 -     1.81: 48
  Bond restraints: 8015
  Sorted by residual:
  bond pdb=" O3'  DT E  49 "
       pdb=" P    DG E  50 "
    ideal  model  delta    sigma   weight residual
    1.607  1.675 -0.068 1.50e-02 4.44e+03 2.08e+01
  bond pdb=" N   ILE B 528 "
       pdb=" CA  ILE B 528 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 8.60e-03 1.35e+04 1.96e+01
  bond pdb=" N   ASN B 475 "
       pdb=" CA  ASN B 475 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 8.30e-03 1.45e+04 1.79e+01
  bond pdb=" N   VAL D 509 "
       pdb=" CA  VAL D 509 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.037 1.14e-02 7.69e+03 1.07e+01
  bond pdb=" N   VAL B 595 "
       pdb=" CA  VAL B 595 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.14e-02 7.69e+03 1.06e+01
  ... (remaining 8010 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 9076
        1.92 -     3.83: 1928
        3.83 -     5.75: 238
        5.75 -     7.66: 128
        7.66 -     9.58: 5
  Bond angle restraints: 11375
  Sorted by residual:
  angle pdb=" C4'  DG F  56 "
        pdb=" C3'  DG F  56 "
        pdb=" O3'  DG F  56 "
      ideal   model   delta    sigma   weight residual
     110.00  119.58   -9.58 1.50e+00 4.44e-01 4.08e+01
  angle pdb=" O3'  DC F  49 "
        pdb=" C3'  DC F  49 "
        pdb=" C2'  DC F  49 "
      ideal   model   delta    sigma   weight residual
     111.50  102.42    9.08 1.50e+00 4.44e-01 3.66e+01
  angle pdb=" C4'  DT F  54 "
        pdb=" C3'  DT F  54 "
        pdb=" O3'  DT F  54 "
      ideal   model   delta    sigma   weight residual
     110.00  118.69   -8.69 1.50e+00 4.44e-01 3.36e+01
  angle pdb=" O3'  DT E  11 "
        pdb=" P    DC E  12 "
        pdb=" O5'  DC E  12 "
      ideal   model   delta    sigma   weight residual
     104.00   96.20    7.80 1.50e+00 4.44e-01 2.70e+01
  angle pdb=" N   THR B 590 "
        pdb=" CA  THR B 590 "
        pdb=" C   THR B 590 "
      ideal   model   delta    sigma   weight residual
     114.04  108.31    5.73 1.24e+00 6.50e-01 2.14e+01
  ... (remaining 11370 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 3931
       35.82 -    71.64: 527
       71.64 -   107.45: 9
      107.45 -   143.27: 7
      143.27 -   179.09: 2
  Dihedral angle restraints: 4476
    sinusoidal: 2619
      harmonic: 1857
  Sorted by residual:
  dihedral pdb=" C4'  DA E  19 "
           pdb=" C3'  DA E  19 "
           pdb=" O3'  DA E  19 "
           pdb=" P    DT E  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.09 -179.09     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA E  55 "
           pdb=" C3'  DA E  55 "
           pdb=" O3'  DA E  55 "
           pdb=" P    DG E  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   70.89  149.11     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" C4'  DG E  13 "
           pdb=" C3'  DG E  13 "
           pdb=" O3'  DG E  13 "
           pdb=" P    DA E  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.63  139.37     1      3.50e+01 8.16e-04 1.38e+01
  ... (remaining 4473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 946
       0.125 -    0.251: 165
       0.251 -    0.376: 6
       0.376 -    0.501: 81
       0.501 -    0.626: 28
  Chirality restraints: 1226
  Sorted by residual:
  chirality pdb=" P    DT E   1 "
            pdb=" OP1  DT E   1 "
            pdb=" OP2  DT E   1 "
            pdb=" O5'  DT E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.97   -0.63 2.00e-01 2.50e+01 9.80e+00
  chirality pdb=" P    DA F   3 "
            pdb=" OP1  DA F   3 "
            pdb=" OP2  DA F   3 "
            pdb=" O5'  DA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.96   -0.61 2.00e-01 2.50e+01 9.34e+00
  chirality pdb=" P    DA E  37 "
            pdb=" OP1  DA E  37 "
            pdb=" OP2  DA E  37 "
            pdb=" O5'  DA E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.95   -0.60 2.00e-01 2.50e+01 9.09e+00
  ... (remaining 1223 not shown)

  Planarity restraints: 1071
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT F  59 "    0.007 2.00e-02 2.50e+03   1.02e-02 2.62e+00
        pdb=" N1   DT F  59 "    0.006 2.00e-02 2.50e+03
        pdb=" C2   DT F  59 "   -0.014 2.00e-02 2.50e+03
        pdb=" O2   DT F  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3   DT F  59 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DT F  59 "    0.018 2.00e-02 2.50e+03
        pdb=" O4   DT F  59 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DT F  59 "    0.008 2.00e-02 2.50e+03
        pdb=" C7   DT F  59 "   -0.016 2.00e-02 2.50e+03
        pdb=" C6   DT F  59 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA F  42 "   -0.014 2.00e-02 2.50e+03   8.70e-03 2.08e+00
        pdb=" N9   DA F  42 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DA F  42 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7   DA F  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DA F  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA F  42 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA F  42 "    0.000 2.00e-02 2.50e+03
        pdb=" N1   DA F  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA F  42 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA F  42 "    0.003 2.00e-02 2.50e+03
        pdb=" C4   DA F  42 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC E  29 "    0.018 2.00e-02 2.50e+03   8.96e-03 1.81e+00
        pdb=" N1   DC E  29 "   -0.016 2.00e-02 2.50e+03
        pdb=" C2   DC E  29 "    0.003 2.00e-02 2.50e+03
        pdb=" O2   DC E  29 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DC E  29 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DC E  29 "    0.000 2.00e-02 2.50e+03
        pdb=" N4   DC E  29 "    0.009 2.00e-02 2.50e+03
        pdb=" C5   DC E  29 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DC E  29 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1068 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 2379
        2.83 -     3.35: 8955
        3.35 -     3.86: 16531
        3.86 -     4.38: 18685
        4.38 -     4.90: 25868
  Nonbonded interactions: 72418
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS D 586 "
            pdb=" O5'  DC E  12 "
     model   vdw
     2.312 3.120
  nonbonded pdb=" NH1 ARG C 538 "
            pdb=" OP1  DA E  21 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" NH2 ARG D 522 "
            pdb=" OP2  DT F  46 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" O   SER C 447 "
            pdb=" O3'  DC E  27 "
     model   vdw
     2.397 3.040
  nonbonded pdb=" N   GLY B 454 "
            pdb=" OP1  DT E  49 "
     model   vdw
     2.401 3.120
  ... (remaining 72413 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 454 through 613)
  selection = (chain 'B' and resid 454 through 613)
  selection = (chain 'C' and resid 454 through 613)
  selection = (chain 'D' and resid 454 through 613)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.140
  Find NCS groups from input model:        0.090
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5202
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      :  0.013   0.068   8015  Z= 0.868
  Angle     :  1.628   9.577  11375  Z= 1.085
  Chirality :  0.168   0.626   1226
  Planarity :  0.002   0.010   1071
  Dihedral  : 24.341 179.086   3302
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 57.86
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  5.85 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  :  5.32 %
    Favored  : 89.91 %
  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 are not related in a simple way.
  whole: -1.17 (0.30), residues: 667
  helix:  1.70 (0.28), residues: 198
  sheet: -2.71 (0.49), residues: 78
  loop : -1.77 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 486 
 TYR   0.004   0.001   TYR D 510 
 PHE   0.008   0.001   PHE D 571 
 TRP   0.007   0.001   TRP D 503 
 HIS   0.003   0.001   HIS A 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.01303 ( 8015)
  covalent geometry    : angle       1.62778 (11375)
  hydrogen bonds       : bond        0.22949 (  362)
  hydrogen bonds       : angle      12.82478 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 5
  residues processed: 201
  average time/residue: 0.0961
  time to fit residues: 24.7344
Evaluate side-chains
  98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  583 VAL
Chi-restraints excluded: chain C residue  441 ASP
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain D residue  541 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 475 ASN
B 475 ASN
** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 HIS
** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 480 ASN
D 519 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.086502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.064897 restraints weight = 31683.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.82
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.5029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8015  Z= 0.245
  Angle     :  0.852   9.464  11375  Z= 0.466
  Chirality :  0.048   0.238   1226
  Planarity :  0.006   0.036   1071
  Dihedral  : 29.127 169.541   2061
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 21.49
  Ramachandran Plot:
    Outliers :  0.60 %
    Allowed  :  5.25 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  6.61 %
    Allowed  : 15.23 %
    Favored  : 78.17 %
  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 are not related in a simple way.
  whole: -0.39 (0.32), residues: 667
  helix:  2.50 (0.33), residues: 212
  sheet: -2.47 (0.48), residues: 78
  loop : -1.47 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 491 
 TYR   0.021   0.003   TYR B 510 
 PHE   0.015   0.002   PHE A 562 
 TRP   0.025   0.003   TRP A 464 
 HIS   0.007   0.002   HIS B 569 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 8015)
  covalent geometry    : angle       0.85210 (11375)
  hydrogen bonds       : bond        0.07940 (  362)
  hydrogen bonds       : angle       5.70284 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 96
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8028 (m-30) cc_final: 0.7809 (m-30)
REVERT: B  475 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6781 (m-40)
REVERT: B  580 LYS cc_start: 0.7267 (mmtm) cc_final: 0.6644 (ttmm)
REVERT: C  605 ASP cc_start: 0.8172 (t0) cc_final: 0.7461 (m-30)
REVERT: C  613 MET cc_start: 0.6641 (mpp) cc_final: 0.5825 (mpp)
REVERT: D  479 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8717 (tm-30)
REVERT: D  609 TRP cc_start: 0.5257 (t-100) cc_final: 0.5021 (t-100)
  outliers start: 36
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0764
  time to fit residues: 13.1025
Evaluate side-chains
  97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 78
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain B residue  475 ASN
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  537 SER
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain C residue  441 ASP
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  537 SER
Chi-restraints excluded: chain D residue  541 PHE
Chi-restraints excluded: chain D residue  585 THR
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 43 optimal weight:    0.0970
   chunk 44 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN
C 480 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.079487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.057729 restraints weight = 31201.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 3.65
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.6586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8015  Z= 0.220
  Angle     :  0.774   8.674  11375  Z= 0.427
  Chirality :  0.043   0.175   1226
  Planarity :  0.006   0.076   1071
  Dihedral  : 29.002 151.966   2060
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 19.36
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.45 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 17.06 %
    Favored  : 77.80 %
  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 are not related in a simple way.
  whole: -0.60 (0.31), residues: 667
  helix:  2.14 (0.33), residues: 206
  sheet: -2.19 (0.48), residues: 79
  loop : -1.51 (0.30), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 469 
 TYR   0.018   0.002   TYR A 518 
 PHE   0.020   0.003   PHE A 562 
 TRP   0.017   0.003   TRP A 464 
 HIS   0.003   0.001   HIS C 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 8015)
  covalent geometry    : angle       0.77370 (11375)
  hydrogen bonds       : bond        0.07395 (  362)
  hydrogen bonds       : angle       5.30819 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  573 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8882 (tt0)
REVERT: A  577 ASP cc_start: 0.8467 (m-30) cc_final: 0.8262 (m-30)
REVERT: A  605 ASP cc_start: 0.8245 (m-30) cc_final: 0.8000 (m-30)
REVERT: C  575 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8494 (tt)
REVERT: C  605 ASP cc_start: 0.8334 (t0) cc_final: 0.7816 (m-30)
REVERT: D  609 TRP cc_start: 0.5541 (t-100) cc_final: 0.5093 (t-100)
  outliers start: 28
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0654
  time to fit residues: 10.0694
Evaluate side-chains
  94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  575 LEU
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  541 PHE
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:   10.0000
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 1 optimal weight:    0.4980
   chunk 51 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.4030 r_free = 0.4030 target = 0.078635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.056868 restraints weight = 31642.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 3.66
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.7335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8015  Z= 0.189
  Angle     :  0.713   7.852  11375  Z= 0.397
  Chirality :  0.040   0.148   1226
  Planarity :  0.006   0.068   1071
  Dihedral  : 29.263 165.570   2057
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 15.66
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.60 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.08 %
    Favored  : 77.98 %
  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 are not related in a simple way.
  whole: -0.22 (0.32), residues: 667
  helix:  2.39 (0.34), residues: 208
  sheet: -1.48 (0.49), residues: 81
  loop : -1.37 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 496 
 TYR   0.014   0.002   TYR A 518 
 PHE   0.019   0.002   PHE A 562 
 TRP   0.012   0.002   TRP A 464 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 8015)
  covalent geometry    : angle       0.71296 (11375)
  hydrogen bonds       : bond        0.06694 (  362)
  hydrogen bonds       : angle       4.72151 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8201 (m-30) cc_final: 0.7947 (m-30)
REVERT: C  605 ASP cc_start: 0.8332 (t0) cc_final: 0.7844 (m-30)
REVERT: D  609 TRP cc_start: 0.5552 (t-100) cc_final: 0.5040 (t-100)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0650
  time to fit residues: 9.1461
Evaluate side-chains
  92 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  541 PHE
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 69 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 3 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN
C 480 ASN
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.074570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.053047 restraints weight = 31567.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 3.57
r_work: 0.3149 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.8137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8015  Z= 0.230
  Angle     :  0.743   7.755  11375  Z= 0.413
  Chirality :  0.042   0.159   1226
  Planarity :  0.007   0.065   1071
  Dihedral  : 29.414 160.792   2057
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.80 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 17.98 %
    Favored  : 77.06 %
  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 are not related in a simple way.
  whole: -0.36 (0.32), residues: 667
  helix:  2.05 (0.34), residues: 206
  sheet: -0.88 (0.52), residues: 74
  loop : -1.47 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 469 
 TYR   0.020   0.002   TYR A 518 
 PHE   0.020   0.002   PHE A 562 
 TRP   0.014   0.002   TRP A 464 
 HIS   0.003   0.001   HIS C 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00521 ( 8015)
  covalent geometry    : angle       0.74283 (11375)
  hydrogen bonds       : bond        0.07340 (  362)
  hydrogen bonds       : angle       4.95336 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 80
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ASP cc_start: 0.8709 (m-30) cc_final: 0.8486 (m-30)
REVERT: A  605 ASP cc_start: 0.8429 (m-30) cc_final: 0.8135 (m-30)
REVERT: C  500 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7391 (mp0)
REVERT: C  575 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8494 (tt)
REVERT: C  605 ASP cc_start: 0.8706 (t0) cc_final: 0.8166 (m-30)
REVERT: D  609 TRP cc_start: 0.5835 (t-100) cc_final: 0.5237 (t-100)
  outliers start: 27
  outliers final: 22
  residues processed: 96
  average time/residue: 0.0658
  time to fit residues: 9.2583
Evaluate side-chains
  94 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  575 LEU
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  537 SER
Chi-restraints excluded: chain D residue  541 PHE
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  606 LEU
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 56 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   chunk 30 optimal weight:    7.9990
   chunk 44 optimal weight:    0.0980
   chunk 12 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0010
   chunk 26 optimal weight:    0.0030
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.3796

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.077994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.056702 restraints weight = 31167.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 3.58
r_work: 0.3255 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.8288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8015  Z= 0.160
  Angle     :  0.701   7.464  11375  Z= 0.386
  Chirality :  0.040   0.151   1226
  Planarity :  0.006   0.067   1071
  Dihedral  : 29.308 163.692   2057
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.40 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.37 %
    Favored  : 76.88 %
  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 are not related in a simple way.
  whole: -0.05 (0.33), residues: 667
  helix:  2.33 (0.35), residues: 215
  sheet: -0.84 (0.52), residues: 80
  loop : -1.36 (0.31), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 496 
 TYR   0.008   0.002   TYR A 518 
 PHE   0.015   0.002   PHE C 508 
 TRP   0.008   0.001   TRP B 464 
 HIS   0.004   0.001   HIS D 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8015)
  covalent geometry    : angle       0.70053 (11375)
  hydrogen bonds       : bond        0.06127 (  362)
  hydrogen bonds       : angle       4.55787 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8244 (m-30) cc_final: 0.7951 (m-30)
REVERT: C  500 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7512 (mp0)
REVERT: C  605 ASP cc_start: 0.8638 (t0) cc_final: 0.8117 (m-30)
REVERT: C  613 MET cc_start: 0.6989 (mpp) cc_final: 0.6559 (mmp)
REVERT: D  609 TRP cc_start: 0.5955 (t-100) cc_final: 0.5384 (t-100)
  outliers start: 15
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0581
  time to fit residues: 7.9977
Evaluate side-chains
  87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  610 PHE
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  583 VAL
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 57 optimal weight:    8.9990
   chunk 65 optimal weight:    0.4980
   chunk 69 optimal weight:    5.9990
   chunk 0 optimal weight:   30.0000
   chunk 58 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.076982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.055907 restraints weight = 31318.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.56
r_work: 0.3231 rms_B_bonded: 4.84 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.8571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8015  Z= 0.166
  Angle     :  0.697   8.001  11375  Z= 0.384
  Chirality :  0.040   0.159   1226
  Planarity :  0.007   0.080   1071
  Dihedral  : 29.352 163.843   2055
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.35 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.92 %
    Favored  : 75.96 %
  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 are not related in a simple way.
  whole:  0.08 (0.33), residues: 667
  helix:  2.42 (0.35), residues: 210
  sheet: -0.61 (0.54), residues: 77
  loop : -1.24 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 594 
 TYR   0.009   0.001   TYR A 518 
 PHE   0.018   0.002   PHE A 562 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8015)
  covalent geometry    : angle       0.69740 (11375)
  hydrogen bonds       : bond        0.06277 (  362)
  hydrogen bonds       : angle       4.53647 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  577 ASP cc_start: 0.8701 (m-30) cc_final: 0.8473 (m-30)
REVERT: A  605 ASP cc_start: 0.8270 (m-30) cc_final: 0.7945 (m-30)
REVERT: C  500 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7506 (mp0)
REVERT: C  605 ASP cc_start: 0.8639 (t0) cc_final: 0.8127 (m-30)
REVERT: D  609 TRP cc_start: 0.6063 (t-100) cc_final: 0.5440 (t-100)
  outliers start: 17
  outliers final: 15
  residues processed: 88
  average time/residue: 0.0626
  time to fit residues: 8.2684
Evaluate side-chains
  89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain B residue  585 THR
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  537 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 3 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.077382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.056406 restraints weight = 31569.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.60
r_work: 0.3245 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.8806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8015  Z= 0.163
  Angle     :  0.696   8.811  11375  Z= 0.382
  Chirality :  0.040   0.219   1226
  Planarity :  0.007   0.076   1071
  Dihedral  : 29.353 165.783   2055
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  5.40 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.47 %
    Favored  : 75.78 %
  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 are not related in a simple way.
  whole:  0.06 (0.33), residues: 667
  helix:  2.27 (0.35), residues: 210
  sheet: -0.48 (0.54), residues: 77
  loop : -1.20 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 594 
 TYR   0.011   0.001   TYR A 518 
 PHE   0.016   0.001   PHE A 562 
 TRP   0.009   0.001   TRP A 464 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8015)
  covalent geometry    : angle       0.69599 (11375)
  hydrogen bonds       : bond        0.06059 (  362)
  hydrogen bonds       : angle       4.46578 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8324 (m-30) cc_final: 0.7982 (m-30)
REVERT: C  500 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7581 (mp0)
REVERT: C  605 ASP cc_start: 0.8617 (t0) cc_final: 0.8088 (m-30)
REVERT: C  613 MET cc_start: 0.6878 (mpp) cc_final: 0.5234 (mmp)
REVERT: D  609 TRP cc_start: 0.6085 (t-100) cc_final: 0.5449 (t-100)
  outliers start: 15
  outliers final: 14
  residues processed: 92
  average time/residue: 0.0606
  time to fit residues: 8.3748
Evaluate side-chains
  90 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 76
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 8 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 72 optimal weight:    5.9990
   chunk 62 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 50 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.077334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.055897 restraints weight = 31495.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 3.68
r_work: 0.3231 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.8971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8015  Z= 0.164
  Angle     :  0.711   9.287  11375  Z= 0.390
  Chirality :  0.040   0.195   1226
  Planarity :  0.007   0.068   1071
  Dihedral  : 29.417 169.561   2055
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  7.50 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.47 %
    Favored  : 75.96 %
  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 are not related in a simple way.
  whole:  0.06 (0.33), residues: 667
  helix:  2.25 (0.35), residues: 210
  sheet: -0.80 (0.51), residues: 85
  loop : -1.11 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 594 
 TYR   0.009   0.001   TYR A 518 
 PHE   0.017   0.001   PHE A 562 
 TRP   0.008   0.001   TRP A 464 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8015)
  covalent geometry    : angle       0.71148 (11375)
  hydrogen bonds       : bond        0.06051 (  362)
  hydrogen bonds       : angle       4.47352 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8296 (m-30) cc_final: 0.7951 (m-30)
REVERT: C  500 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7662 (mp0)
REVERT: C  605 ASP cc_start: 0.8624 (t0) cc_final: 0.8116 (m-30)
REVERT: D  609 TRP cc_start: 0.6199 (t-100) cc_final: 0.5530 (t-100)
  outliers start: 14
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0574
  time to fit residues: 7.3519
Evaluate side-chains
  87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  537 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B 567 GLN
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.074443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.053371 restraints weight = 32533.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 3.71
r_work: 0.3139 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.9302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8015  Z= 0.210
  Angle     :  0.750   7.699  11375  Z= 0.410
  Chirality :  0.041   0.190   1226
  Planarity :  0.007   0.075   1071
  Dihedral  : 29.484 170.482   2055
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.10 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.92 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.52 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.32), residues: 667
  helix:  1.96 (0.34), residues: 208
  sheet: -0.57 (0.52), residues: 76
  loop : -1.30 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 486 
 TYR   0.012   0.002   TYR A 518 
 PHE   0.021   0.002   PHE A 562 
 TRP   0.015   0.002   TRP A 464 
 HIS   0.002   0.001   HIS C 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 8015)
  covalent geometry    : angle       0.74955 (11375)
  hydrogen bonds       : bond        0.06846 (  362)
  hydrogen bonds       : angle       4.72095 ( 1014)

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

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

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1334 Ramachandran restraints generated.
    667 Oldfield, 0 Emsley, 667 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  605 ASP cc_start: 0.8401 (m-30) cc_final: 0.8047 (m-30)
REVERT: C  500 GLU cc_start: 0.8549 (mm-30) cc_final: 0.7864 (mp0)
REVERT: C  605 ASP cc_start: 0.8676 (t0) cc_final: 0.8159 (m-30)
REVERT: C  613 MET cc_start: 0.7136 (mpp) cc_final: 0.5691 (mmt)
REVERT: D  488 LEU cc_start: 0.8802 (mm) cc_final: 0.8598 (mm)
REVERT: D  609 TRP cc_start: 0.6251 (t-100) cc_final: 0.5682 (t-100)
  outliers start: 16
  outliers final: 16
  residues processed: 88
  average time/residue: 0.0577
  time to fit residues: 7.7583
Evaluate side-chains
  87 residues out of total 545 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  562 PHE
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain B residue  494 VAL
Chi-restraints excluded: chain B residue  507 VAL
Chi-restraints excluded: chain C residue  460 LYS
Chi-restraints excluded: chain C residue  494 VAL
Chi-restraints excluded: chain C residue  557 SER
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  604 VAL
Chi-restraints excluded: chain D residue  494 VAL
Chi-restraints excluded: chain D residue  537 SER
Chi-restraints excluded: chain D residue  597 VAL
Chi-restraints excluded: chain D residue  610 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 48 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   chunk 67 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0020
   chunk 59 optimal weight:    0.6980
   chunk 73 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    0.6390

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

Flipped N/Q/H residues before XYZ refinement:
** D 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.076868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.055497 restraints weight = 32240.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 3.72
r_work: 0.3235 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.9436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8015  Z= 0.160
  Angle     :  0.708   9.156  11375  Z= 0.386
  Chirality :  0.040   0.205   1226
  Planarity :  0.007   0.067   1071
  Dihedral  : 29.249 171.166   2055
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.30 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.28 %
    Favored  : 75.96 %
  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 are not related in a simple way.
  whole: -0.09 (0.33), residues: 667
  helix:  2.16 (0.35), residues: 209
  sheet: -0.79 (0.52), residues: 85
  loop : -1.24 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 486 
 TYR   0.009   0.001   TYR A 518 
 PHE   0.016   0.001   PHE A 562 
 TRP   0.009   0.001   TRP D 464 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8015)
  covalent geometry    : angle       0.70782 (11375)
  hydrogen bonds       : bond        0.05901 (  362)
  hydrogen bonds       : angle       4.49874 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2163.49 seconds
wall clock time: 37 minutes 38.72 seconds (2258.72 seconds total)