Starting phenix.real_space_refine
on Tue Feb  3 18:52:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s2u_54511/02_2026/9s2u_54511.cif"
  }
  resolution = 3.2
  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=   0.011
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: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    3975      2.51       5
     N    1030      2.21       5
     O    1123      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6157
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 5564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 738, 5564
          Classifications: {'peptide': 738}
          Link IDs: {'PTRANS': 34, 'TRANS': 703}
    Chain: "I"
      Number of atoms: 593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 593
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 3, 'TRANS': 74}
  Time building chain proxies: 1.35, per 1000 atoms: 0.22
  Number of scatterers: 6157
  At special positions: 0
  Unit cell: (64.94, 75.445, 133.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1123      8.00
     N    1030      7.00
     C    3975      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: 0.65
  Conformation dependent library (CDL) restraints added in 204.1 milliseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 3 sheets defined
      70.3% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'D' and resid 23 through 29
    Processing helix  chain 'D' and resid 31 through 49
      removed outlier: 3.682A  pdb=" N   THR D  49 " --> pdb=" O   VAL D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 60
    Processing helix  chain 'D' and resid 69 through 83
    Processing helix  chain 'D' and resid 102 through 119
    Processing helix  chain 'D' and resid 132 through 139
      removed outlier: 5.339A  pdb=" N   THR D 137 " --> pdb=" O   LEU D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 159 through 176
    Processing helix  chain 'D' and resid 188 through 223
      removed outlier: 4.293A  pdb=" N   GLN D 205 " --> pdb=" O   ASP D 201 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   VAL D 206 " --> pdb=" O   ARG D 202 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU D 221 " --> pdb=" O   VAL D 217 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 226 through 253
      removed outlier: 3.652A  pdb=" N   MET D 232 " --> pdb=" O   THR D 228 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS D 253 " --> pdb=" O   PHE D 249 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 259 through 291
    Processing helix  chain 'D' and resid 294 through 323
      removed outlier: 3.655A  pdb=" N   TYR D 300 " --> pdb=" O   GLU D 296 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   HIS D 308 " --> pdb=" O   GLY D 304 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   VAL D 309 " --> pdb=" O   GLY D 305 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   THR D 321 " --> pdb=" O   ILE D 317 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 329 through 362
      removed outlier: 4.455A  pdb=" N   LEU D 335 " --> pdb=" O   TYR D 331 " (cutoff:3.500A)
      Proline residue:  D 338  - end of helix
      Proline residue:  D 355  - end of helix
    Processing helix  chain 'D' and resid 377 through 385
      removed outlier: 3.900A  pdb=" N   VAL D 382 " --> pdb=" O   GLY D 378 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY D 383 " --> pdb=" O   TRP D 379 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA D 384 " --> pdb=" O   ARG D 380 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ALA D 385 " --> pdb=" O   LYS D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 389 through 406
      removed outlier: 3.505A  pdb=" N   ILE D 393 " --> pdb=" O   TRP D 389 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 407 through 411
    Processing helix  chain 'D' and resid 417 through 421
    Processing helix  chain 'D' and resid 425 through 438
      removed outlier: 3.670A  pdb=" N   HIS D 437 " --> pdb=" O   ALA D 433 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 458 through 475
      removed outlier: 3.850A  pdb=" N   ASN D 466 " --> pdb=" O   PHE D 462 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   LYS D 467 " --> pdb=" O   LEU D 463 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   ILE D 468 " --> pdb=" O   VAL D 464 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   ALA D 469 " --> pdb=" O   ILE D 465 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   VAL D 475 " --> pdb=" O   ALA D 471 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 698 through 706
      removed outlier: 4.032A  pdb=" N   GLY D 704 " --> pdb=" O   ASP D 700 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 728 through 747
      removed outlier: 4.240A  pdb=" N   ILE D 735 " --> pdb=" O   GLY D 731 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   ALA D 736 " --> pdb=" O   ILE D 732 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   LYS D 737 " --> pdb=" O   ALA D 733 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 761 through 795
      removed outlier: 3.774A  pdb=" N   GLY D 771 " --> pdb=" O   ASP D 767 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ASN D 772 " --> pdb=" O   LEU D 768 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   THR D 773 " --> pdb=" O   SER D 769 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   TYR D 774 " --> pdb=" O   ASP D 770 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   LEU D 784 " --> pdb=" O   GLY D 780 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 798 through 824
      removed outlier: 3.506A  pdb=" N   ALA D 802 " --> pdb=" O   VAL D 798 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL D 805 " --> pdb=" O   ALA D 801 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL D 808 " --> pdb=" O   ILE D 804 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLY D 813 " --> pdb=" O   VAL D 809 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ALA D 814 " --> pdb=" O   LEU D 810 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 833 through 861
      removed outlier: 3.889A  pdb=" N   ALA D 839 " --> pdb=" O   VAL D 835 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 862 through 864
      No H-bonds generated for 'chain 'D' and resid 862 through 864'
    Processing helix  chain 'D' and resid 865 through 894
      removed outlier: 5.102A  pdb=" N   SER D 879 " --> pdb=" O   GLY D 875 " (cutoff:3.500A)
      removed outlier: 5.535A  pdb=" N   VAL D 880 " --> pdb=" O   GLY D 876 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 895 through 898
    Processing helix  chain 'D' and resid 900 through 920
    Processing helix  chain 'D' and resid 924 through 933
    Processing helix  chain 'D' and resid 938 through 942
    Processing helix  chain 'I' and resid 4 through 21
    Processing helix  chain 'I' and resid 23 through 27
      removed outlier: 3.753A  pdb=" N   GLU I  26 " --> pdb=" O   GLU I  23 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 33 through 38
    Processing helix  chain 'I' and resid 40 through 55
    Processing helix  chain 'I' and resid 69 through 80
    Processing sheet with id=AA1, first strand: chain 'D' and resid 123 through 127
      removed outlier: 3.971A  pdb=" N   GLN D 150 " --> pdb=" O   GLN D 127 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 446 through 448
    Processing sheet with id=AA3, first strand: chain 'D' and resid 480 through 482
      removed outlier: 4.025A  pdb=" N   ARG D 480 " --> pdb=" O   SER D 721 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1138
        1.33 -     1.45: 1461
        1.45 -     1.57: 3621
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 6276
  Sorted by residual:
  bond pdb=" C   ALA D 272 "
       pdb=" O   ALA D 272 "
    ideal  model  delta    sigma   weight residual
    1.237  1.204  0.032 1.17e-02 7.31e+03 7.68e+00
  bond pdb=" CB  ILE D 804 "
       pdb=" CG1 ILE D 804 "
    ideal  model  delta    sigma   weight residual
    1.530  1.478  0.052 2.00e-02 2.50e+03 6.80e+00
  bond pdb=" CA  SER D 811 "
       pdb=" CB  SER D 811 "
    ideal  model  delta    sigma   weight residual
    1.529  1.487  0.042 1.74e-02 3.30e+03 5.79e+00
  bond pdb=" CA  SER D 877 "
       pdb=" CB  SER D 877 "
    ideal  model  delta    sigma   weight residual
    1.537  1.503  0.034 1.41e-02 5.03e+03 5.66e+00
  bond pdb=" C   VAL D 186 "
       pdb=" O   VAL D 186 "
    ideal  model  delta    sigma   weight residual
    1.238  1.213  0.025 1.10e-02 8.26e+03 5.17e+00
  ... (remaining 6271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 7949
        1.33 -     2.67: 532
        2.67 -     4.00: 49
        4.00 -     5.33: 12
        5.33 -     6.67: 2
  Bond angle restraints: 8544
  Sorted by residual:
  angle pdb=" NE  ARG D 922 "
        pdb=" CZ  ARG D 922 "
        pdb=" NH1 ARG D 922 "
      ideal   model   delta    sigma   weight residual
     121.50  117.04    4.46 1.00e+00 1.00e+00 1.99e+01
  angle pdb=" NH1 ARG D 922 "
        pdb=" CZ  ARG D 922 "
        pdb=" NH2 ARG D 922 "
      ideal   model   delta    sigma   weight residual
     119.30  124.56   -5.26 1.30e+00 5.92e-01 1.64e+01
  angle pdb=" OD1 ASN D 851 "
        pdb=" CG  ASN D 851 "
        pdb=" ND2 ASN D 851 "
      ideal   model   delta    sigma   weight residual
     122.60  120.11    2.49 1.00e+00 1.00e+00 6.20e+00
  angle pdb=" CA  ARG D  21 "
        pdb=" C   ARG D  21 "
        pdb=" N   PRO D  22 "
      ideal   model   delta    sigma   weight residual
     116.90  120.62   -3.72 1.50e+00 4.44e-01 6.15e+00
  angle pdb=" N   MET D  64 "
        pdb=" CA  MET D  64 "
        pdb=" C   MET D  64 "
      ideal   model   delta    sigma   weight residual
     113.38  110.63    2.75 1.23e+00 6.61e-01 5.01e+00
  ... (remaining 8539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.75: 3372
       17.75 -    35.50: 299
       35.50 -    53.24: 47
       53.24 -    70.99: 9
       70.99 -    88.74: 8
  Dihedral angle restraints: 3735
    sinusoidal: 1412
      harmonic: 2323
  Sorted by residual:
  dihedral pdb=" CA  CYS D 323 "
           pdb=" C   CYS D 323 "
           pdb=" N   LEU D 324 "
           pdb=" CA  LEU D 324 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  THR D 334 "
           pdb=" C   THR D 334 "
           pdb=" N   LEU D 335 "
           pdb=" CA  LEU D 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.59   21.41     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LEU D 324 "
           pdb=" C   LEU D 324 "
           pdb=" N   SER D 325 "
           pdb=" CA  SER D 325 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.64  -20.36     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 3732 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 590
       0.045 -    0.090: 317
       0.090 -    0.134: 92
       0.134 -    0.179: 26
       0.179 -    0.224: 3
  Chirality restraints: 1028
  Sorted by residual:
  chirality pdb=" CA  PRO D 355 "
            pdb=" N   PRO D 355 "
            pdb=" C   PRO D 355 "
            pdb=" CB  PRO D 355 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  PRO D 927 "
            pdb=" N   PRO D 927 "
            pdb=" C   PRO D 927 "
            pdb=" CB  PRO D 927 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CB  ILE D 804 "
            pdb=" CA  ILE D 804 "
            pdb=" CG1 ILE D 804 "
            pdb=" CG2 ILE D 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.36e-01
  ... (remaining 1025 not shown)

  Planarity restraints: 1082
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 431 "    0.025 2.00e-02 2.50e+03   2.43e-02 1.18e+01
        pdb=" CG  TYR D 431 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 431 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 431 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 431 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 431 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 431 "    0.054 2.00e-02 2.50e+03
        pdb=" OH  TYR D 431 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D 890 "    0.026 2.00e-02 2.50e+03   2.18e-02 8.31e+00
        pdb=" CG  PHE D 890 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 PHE D 890 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD2 PHE D 890 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE D 890 "    0.029 2.00e-02 2.50e+03
        pdb=" CE2 PHE D 890 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE D 890 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 379 "   -0.025 2.00e-02 2.50e+03   1.73e-02 7.51e+00
        pdb=" CG  TRP D 379 "    0.003 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 379 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 379 "   -0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 379 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 379 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 379 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 379 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 379 "    0.030 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 379 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1079 not shown)

  Histogram of nonbonded interaction distances:
        2.54 -     3.01: 3491
        3.01 -     3.48: 7006
        3.48 -     3.96: 9960
        3.96 -     4.43: 11780
        4.43 -     4.90: 18498
  Nonbonded interactions: 50735
  Sorted by model distance:
  nonbonded pdb=" O   ASN D 772 "
            pdb=" OD1 ASP D 775 "
     model   vdw
     2.538 3.040
  nonbonded pdb=" N   THR D 795 "
            pdb=" O   THR D 795 "
     model   vdw
     2.565 2.496
  nonbonded pdb=" O   SER D 898 "
            pdb=" OG  SER D 898 "
     model   vdw
     2.587 3.040
  nonbonded pdb=" O   MET D 791 "
            pdb=" O   THR D 795 "
     model   vdw
     2.599 3.040
  nonbonded pdb=" O   THR I  20 "
            pdb=" OG1 THR I  20 "
     model   vdw
     2.604 3.040
  ... (remaining 50730 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.820
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.490
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
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      :  0.007   0.052   6276  Z= 0.451
  Angle     :  0.749   6.667   8544  Z= 0.461
  Chirality :  0.058   0.224   1028
  Planarity :  0.006   0.049   1082
  Dihedral  : 14.173  88.739   2245
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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: -0.10 (0.29), residues: 812
  helix:  0.64 (0.23), residues: 520
  sheet: -1.11 (0.86), residues: 35
  loop : -1.26 (0.39), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG D 857 
 TYR   0.054   0.005   TYR D 431 
 PHE   0.038   0.004   PHE D 890 
 TRP   0.030   0.006   TRP D 379 
 HIS   0.018   0.003   HIS D 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00728 ( 6276)
  covalent geometry    : angle       0.74871 ( 8544)
  hydrogen bonds       : bond        0.11987 (  416)
  hydrogen bonds       : angle       6.93516 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7575 (ttm) cc_final: 0.6960 (tmm)
REVERT: D   67 ASP cc_start: 0.7986 (t0) cc_final: 0.7173 (p0)
REVERT: D   80 LYS cc_start: 0.8326 (tptt) cc_final: 0.8114 (pttm)
REVERT: D   92 MET cc_start: 0.8060 (mtt) cc_final: 0.7819 (mtt)
REVERT: D  204 LEU cc_start: 0.7272 (tt) cc_final: 0.6907 (tt)
REVERT: D  205 GLN cc_start: 0.7100 (pt0) cc_final: 0.6590 (pm20)
REVERT: D  327 THR cc_start: 0.7783 (m) cc_final: 0.7263 (p)
REVERT: D  332 PHE cc_start: 0.7870 (m-80) cc_final: 0.7343 (m-80)
REVERT: D  936 TRP cc_start: 0.7460 (m100) cc_final: 0.7196 (m100)
REVERT: I   17 GLU cc_start: 0.8727 (tp30) cc_final: 0.8403 (tp30)
REVERT: I   22 ILE cc_start: 0.8319 (mp) cc_final: 0.7880 (mp)
REVERT: I   23 GLU cc_start: 0.9130 (mp0) cc_final: 0.8856 (mp0)
REVERT: I   36 ASP cc_start: 0.9072 (m-30) cc_final: 0.8814 (m-30)
REVERT: I   37 LEU cc_start: 0.8456 (mm) cc_final: 0.7673 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 189
  average time/residue: 0.0579
  time to fit residues: 14.9730
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.0870
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.4980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
D 117 GLN
D 286 GLN
D 824 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.153901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.134567 restraints weight = 13811.587|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.51
r_work: 0.3850 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6276  Z= 0.146
  Angle     :  0.651   8.030   8544  Z= 0.334
  Chirality :  0.043   0.150   1028
  Planarity :  0.005   0.048   1082
  Dihedral  :  4.556  26.325    870
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.69 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 10.49 %
    Favored  : 87.35 %
  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: -0.21 (0.29), residues: 812
  helix:  0.54 (0.22), residues: 525
  sheet: -0.86 (0.86), residues: 35
  loop : -1.35 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 717 
 TYR   0.019   0.002   TYR D 285 
 PHE   0.016   0.001   PHE I  33 
 TRP   0.005   0.001   TRP D  39 
 HIS   0.002   0.001   HIS D 832 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6276)
  covalent geometry    : angle       0.65067 ( 8544)
  hydrogen bonds       : bond        0.04322 (  416)
  hydrogen bonds       : angle       6.15605 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7629 (ttm) cc_final: 0.6832 (tmm)
REVERT: D   67 ASP cc_start: 0.7534 (t0) cc_final: 0.7058 (p0)
REVERT: D   80 LYS cc_start: 0.8359 (tptt) cc_final: 0.8113 (pttm)
REVERT: D  205 GLN cc_start: 0.6895 (pt0) cc_final: 0.6422 (pm20)
REVERT: D  790 ILE cc_start: 0.6654 (mm) cc_final: 0.6295 (mm)
REVERT: I   23 GLU cc_start: 0.8708 (mp0) cc_final: 0.8360 (mp0)
REVERT: I   37 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7737 (mm)
  outliers start: 14
  outliers final: 9
  residues processed: 142
  average time/residue: 0.0547
  time to fit residues: 10.7376
Evaluate side-chains
  126 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  176 LEU
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  315 LEU
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   37 LEU
Chi-restraints excluded: chain I residue   43 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 65 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0970
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 63 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
D 140 GLN
D 482 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.152889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.133688 restraints weight = 13806.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.4013 rms_B_bonded: 3.38
r_work: 0.3903 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6276  Z= 0.152
  Angle     :  0.635   7.324   8544  Z= 0.328
  Chirality :  0.042   0.151   1028
  Planarity :  0.005   0.055   1082
  Dihedral  :  4.594  27.443    870
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.31 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.97 %
    Favored  : 82.72 %
  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: -0.33 (0.29), residues: 812
  helix:  0.41 (0.22), residues: 526
  sheet: -0.92 (0.84), residues: 35
  loop : -1.30 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  99 
 TYR   0.013   0.001   TYR D 285 
 PHE   0.015   0.002   PHE D 895 
 TRP   0.009   0.001   TRP D 936 
 HIS   0.003   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6276)
  covalent geometry    : angle       0.63470 ( 8544)
  hydrogen bonds       : bond        0.04198 (  416)
  hydrogen bonds       : angle       6.05198 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7695 (ttm) cc_final: 0.6968 (tmm)
REVERT: D   67 ASP cc_start: 0.7546 (t0) cc_final: 0.7138 (p0)
REVERT: D   92 MET cc_start: 0.8459 (mtt) cc_final: 0.7988 (mtt)
REVERT: D  205 GLN cc_start: 0.6773 (pt0) cc_final: 0.6393 (pm20)
REVERT: D  214 VAL cc_start: 0.7388 (OUTLIER) cc_final: 0.6955 (t)
REVERT: D  790 ILE cc_start: 0.6741 (mm) cc_final: 0.6352 (mm)
REVERT: I   31 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6290 (tmtt)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 0.0585
  time to fit residues: 10.8029
Evaluate side-chains
  127 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  214 VAL
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  238 LEU
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  841 ILE
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0570
   chunk 21 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 58 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
D  77 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.152097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.132777 restraints weight = 13997.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 3.44
r_work: 0.3903 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6276  Z= 0.146
  Angle     :  0.656   8.702   8544  Z= 0.332
  Chirality :  0.042   0.170   1028
  Planarity :  0.005   0.056   1082
  Dihedral  :  4.625  27.186    870
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.57 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.97 %
    Favored  : 81.79 %
  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 (0.29), residues: 812
  helix:  0.33 (0.22), residues: 527
  sheet: -0.81 (0.85), residues: 35
  loop : -1.26 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 717 
 TYR   0.012   0.001   TYR D 285 
 PHE   0.014   0.001   PHE D 689 
 TRP   0.012   0.001   TRP D 936 
 HIS   0.003   0.001   HIS D  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6276)
  covalent geometry    : angle       0.65552 ( 8544)
  hydrogen bonds       : bond        0.04054 (  416)
  hydrogen bonds       : angle       5.92540 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7746 (ttm) cc_final: 0.7027 (tmm)
REVERT: D   67 ASP cc_start: 0.7535 (t0) cc_final: 0.7143 (p0)
REVERT: D   92 MET cc_start: 0.8514 (mtt) cc_final: 0.8109 (mtt)
REVERT: D  205 GLN cc_start: 0.6796 (pt0) cc_final: 0.6406 (pm20)
REVERT: D  220 LEU cc_start: 0.5868 (mt) cc_final: 0.5371 (tt)
REVERT: D  790 ILE cc_start: 0.6785 (mm) cc_final: 0.6401 (mm)
REVERT: D  938 TRP cc_start: 0.6472 (m100) cc_final: 0.6223 (m100)
REVERT: I   17 GLU cc_start: 0.8581 (tp30) cc_final: 0.8274 (tp30)
REVERT: I   22 ILE cc_start: 0.8054 (mp) cc_final: 0.7409 (mp)
REVERT: I   23 GLU cc_start: 0.8369 (mp0) cc_final: 0.8127 (mp0)
  outliers start: 21
  outliers final: 11
  residues processed: 137
  average time/residue: 0.0476
  time to fit residues: 9.1654
Evaluate side-chains
  124 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 53 optimal weight:    0.2980
   chunk 42 optimal weight:    0.1980
   chunk 51 optimal weight:    0.0870
   chunk 25 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.4281 r_free = 0.4281 target = 0.152593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.133862 restraints weight = 13925.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.4024 rms_B_bonded: 3.34
r_work: 0.3914 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6276  Z= 0.138
  Angle     :  0.649   9.201   8544  Z= 0.329
  Chirality :  0.042   0.139   1028
  Planarity :  0.005   0.056   1082
  Dihedral  :  4.577  25.554    870
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 17.13 %
    Favored  : 79.63 %
  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: -0.34 (0.29), residues: 812
  helix:  0.33 (0.22), residues: 525
  sheet: -0.84 (0.84), residues: 40
  loop : -1.13 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  99 
 TYR   0.013   0.001   TYR D 285 
 PHE   0.010   0.001   PHE D 303 
 TRP   0.010   0.001   TRP D 936 
 HIS   0.002   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6276)
  covalent geometry    : angle       0.64893 ( 8544)
  hydrogen bonds       : bond        0.03924 (  416)
  hydrogen bonds       : angle       5.84510 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7718 (ttm) cc_final: 0.6997 (tmm)
REVERT: D   67 ASP cc_start: 0.7504 (t0) cc_final: 0.7147 (p0)
REVERT: D   92 MET cc_start: 0.8568 (mtt) cc_final: 0.8234 (mtt)
REVERT: D  205 GLN cc_start: 0.6796 (pt0) cc_final: 0.6422 (pm20)
REVERT: D  220 LEU cc_start: 0.5781 (mt) cc_final: 0.5312 (tt)
REVERT: D  233 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7994 (mm)
REVERT: D  790 ILE cc_start: 0.6714 (mm) cc_final: 0.6345 (mm)
REVERT: D  938 TRP cc_start: 0.6417 (m100) cc_final: 0.5746 (m100)
REVERT: I   17 GLU cc_start: 0.8616 (tp30) cc_final: 0.8306 (tp30)
REVERT: I   22 ILE cc_start: 0.7973 (mp) cc_final: 0.7347 (mp)
REVERT: I   23 GLU cc_start: 0.8417 (mp0) cc_final: 0.8158 (mp0)
  outliers start: 21
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0530
  time to fit residues: 10.2654
Evaluate side-chains
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  346 VAL
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    0.3980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D 482 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.149841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.131264 restraints weight = 13862.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 3.30
r_work: 0.3886 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6276  Z= 0.168
  Angle     :  0.675   8.311   8544  Z= 0.343
  Chirality :  0.043   0.171   1028
  Planarity :  0.005   0.059   1082
  Dihedral  :  4.613  24.054    870
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.06 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.06 %
    Favored  : 78.09 %
  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 are not related in a simple way.
  whole: -0.50 (0.29), residues: 812
  helix:  0.19 (0.22), residues: 525
  sheet: -0.83 (0.85), residues: 40
  loop : -1.18 (0.40), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  99 
 TYR   0.019   0.002   TYR D 299 
 PHE   0.017   0.001   PHE D 689 
 TRP   0.008   0.001   TRP D 936 
 HIS   0.004   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 6276)
  covalent geometry    : angle       0.67503 ( 8544)
  hydrogen bonds       : bond        0.04230 (  416)
  hydrogen bonds       : angle       5.95648 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7738 (ttm) cc_final: 0.6987 (tmm)
REVERT: D   67 ASP cc_start: 0.7500 (t0) cc_final: 0.7119 (p0)
REVERT: D   92 MET cc_start: 0.8629 (mtt) cc_final: 0.8307 (mtt)
REVERT: D  204 LEU cc_start: 0.7046 (tt) cc_final: 0.6755 (tt)
REVERT: D  205 GLN cc_start: 0.6749 (pt0) cc_final: 0.6258 (pm20)
REVERT: D  220 LEU cc_start: 0.5788 (mt) cc_final: 0.5280 (tt)
REVERT: D  233 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7997 (mm)
REVERT: D  368 LEU cc_start: 0.5352 (OUTLIER) cc_final: 0.4996 (mm)
REVERT: D  790 ILE cc_start: 0.6917 (mm) cc_final: 0.6538 (mm)
REVERT: D  938 TRP cc_start: 0.6392 (m100) cc_final: 0.5767 (m100)
REVERT: I   14 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7779 (pt0)
REVERT: I   17 GLU cc_start: 0.8667 (tp30) cc_final: 0.8390 (tp30)
REVERT: I   18 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8134 (mp0)
REVERT: I   22 ILE cc_start: 0.8149 (mp) cc_final: 0.7597 (mp)
REVERT: I   23 GLU cc_start: 0.8462 (mp0) cc_final: 0.8165 (mp0)
  outliers start: 25
  outliers final: 18
  residues processed: 139
  average time/residue: 0.0651
  time to fit residues: 12.7081
Evaluate side-chains
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  238 LEU
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  431 TYR
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  798 VAL
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   64 LEU
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4245 r_free = 0.4245 target = 0.149720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.131239 restraints weight = 13889.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 3.30
r_work: 0.3883 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6276  Z= 0.163
  Angle     :  0.685  11.650   8544  Z= 0.344
  Chirality :  0.043   0.161   1028
  Planarity :  0.005   0.060   1082
  Dihedral  :  4.640  23.493    870
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 18.67 %
    Favored  : 77.62 %
  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: -0.56 (0.29), residues: 812
  helix:  0.12 (0.22), residues: 527
  sheet: -0.88 (0.85), residues: 40
  loop : -1.14 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  99 
 TYR   0.014   0.001   TYR D 285 
 PHE   0.016   0.001   PHE D 689 
 TRP   0.008   0.001   TRP D 936 
 HIS   0.003   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6276)
  covalent geometry    : angle       0.68542 ( 8544)
  hydrogen bonds       : bond        0.04200 (  416)
  hydrogen bonds       : angle       5.95446 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7684 (ttm) cc_final: 0.6990 (tmm)
REVERT: D   67 ASP cc_start: 0.7455 (t0) cc_final: 0.7128 (p0)
REVERT: D   92 MET cc_start: 0.8595 (mtt) cc_final: 0.8389 (mtt)
REVERT: D  205 GLN cc_start: 0.6632 (pt0) cc_final: 0.6195 (pm20)
REVERT: D  220 LEU cc_start: 0.5693 (mt) cc_final: 0.5251 (tt)
REVERT: D  233 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7999 (mm)
REVERT: D  938 TRP cc_start: 0.6396 (m100) cc_final: 0.5816 (m100)
REVERT: I   17 GLU cc_start: 0.8641 (tp30) cc_final: 0.8373 (tp30)
REVERT: I   22 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7681 (mp)
REVERT: I   23 GLU cc_start: 0.8452 (mp0) cc_final: 0.8176 (mp0)
  outliers start: 24
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0594
  time to fit residues: 11.4690
Evaluate side-chains
  132 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  798 VAL
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   22 ILE
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 75 optimal weight:    0.0470
   chunk 62 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.150261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.131641 restraints weight = 13973.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 3.33
r_work: 0.3899 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.3148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6276  Z= 0.153
  Angle     :  0.717  10.061   8544  Z= 0.352
  Chirality :  0.044   0.268   1028
  Planarity :  0.005   0.059   1082
  Dihedral  :  4.675  24.504    870
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.14 %
    Favored  : 77.62 %
  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: -0.51 (0.29), residues: 812
  helix:  0.17 (0.22), residues: 527
  sheet: -0.85 (0.85), residues: 40
  loop : -1.15 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  99 
 TYR   0.022   0.002   TYR D 757 
 PHE   0.015   0.001   PHE D 689 
 TRP   0.009   0.001   TRP D 936 
 HIS   0.003   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6276)
  covalent geometry    : angle       0.71707 ( 8544)
  hydrogen bonds       : bond        0.04181 (  416)
  hydrogen bonds       : angle       5.86786 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7650 (ttm) cc_final: 0.6948 (tmm)
REVERT: D   67 ASP cc_start: 0.7472 (t0) cc_final: 0.7101 (p0)
REVERT: D   92 MET cc_start: 0.8599 (mtt) cc_final: 0.8394 (mtt)
REVERT: D  233 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.8007 (mm)
REVERT: D  368 LEU cc_start: 0.5402 (OUTLIER) cc_final: 0.5037 (mm)
REVERT: D  417 ASP cc_start: 0.8969 (OUTLIER) cc_final: 0.8748 (t0)
REVERT: D  790 ILE cc_start: 0.6797 (mm) cc_final: 0.6366 (mm)
REVERT: D  938 TRP cc_start: 0.6430 (m100) cc_final: 0.5834 (m100)
REVERT: I   17 GLU cc_start: 0.8667 (tp30) cc_final: 0.8435 (tp30)
REVERT: I   22 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7689 (mp)
REVERT: I   23 GLU cc_start: 0.8456 (mp0) cc_final: 0.8173 (mp0)
  outliers start: 21
  outliers final: 16
  residues processed: 132
  average time/residue: 0.0475
  time to fit residues: 8.8698
Evaluate side-chains
  133 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  798 VAL
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   22 ILE
Chi-restraints excluded: chain I residue   28 THR
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0670
   chunk 62 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 43 optimal weight:    0.0670
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.4256

-------------------------------------------------------------------------------
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 = 0.4266 r_free = 0.4266 target = 0.151291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.132923 restraints weight = 13961.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.30
r_work: 0.3910 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6276  Z= 0.146
  Angle     :  0.706  10.658   8544  Z= 0.350
  Chirality :  0.043   0.174   1028
  Planarity :  0.005   0.059   1082
  Dihedral  :  4.676  24.464    870
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.44 %
    Favored  : 77.16 %
  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: -0.46 (0.29), residues: 812
  helix:  0.23 (0.22), residues: 527
  sheet: -0.69 (0.86), residues: 40
  loop : -1.21 (0.40), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  99 
 TYR   0.016   0.002   TYR D 285 
 PHE   0.024   0.001   PHE D 473 
 TRP   0.009   0.001   TRP D 936 
 HIS   0.002   0.000   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6276)
  covalent geometry    : angle       0.70628 ( 8544)
  hydrogen bonds       : bond        0.04058 (  416)
  hydrogen bonds       : angle       5.81864 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7520 (ttm) cc_final: 0.6883 (tmm)
REVERT: D   67 ASP cc_start: 0.7369 (t0) cc_final: 0.7105 (p0)
REVERT: D   92 MET cc_start: 0.8561 (mtt) cc_final: 0.8355 (mtt)
REVERT: D  233 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8088 (mm)
REVERT: D  368 LEU cc_start: 0.5395 (OUTLIER) cc_final: 0.5021 (mm)
REVERT: D  417 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8747 (t0)
REVERT: D  790 ILE cc_start: 0.6587 (mm) cc_final: 0.6156 (mm)
REVERT: D  938 TRP cc_start: 0.6385 (m100) cc_final: 0.5790 (m100)
REVERT: I   17 GLU cc_start: 0.8650 (tp30) cc_final: 0.8430 (tp30)
REVERT: I   22 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7737 (mp)
REVERT: I   23 GLU cc_start: 0.8429 (mp0) cc_final: 0.8153 (mp0)
  outliers start: 22
  outliers final: 16
  residues processed: 130
  average time/residue: 0.0631
  time to fit residues: 11.5595
Evaluate side-chains
  137 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  233 LEU
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  798 VAL
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   22 ILE
Chi-restraints excluded: chain I residue   28 THR
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 67 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0570
   chunk 55 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0770
   chunk 22 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.4056

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.151793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.133160 restraints weight = 13992.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.4022 rms_B_bonded: 3.35
r_work: 0.3917 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   6276  Z= 0.146
  Angle     :  0.726  10.898   8544  Z= 0.358
  Chirality :  0.043   0.191   1028
  Planarity :  0.005   0.059   1082
  Dihedral  :  4.677  24.504    870
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.31 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.29 %
    Favored  : 77.47 %
  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: -0.45 (0.29), residues: 812
  helix:  0.26 (0.22), residues: 526
  sheet: -0.61 (0.87), residues: 40
  loop : -1.28 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  99 
 TYR   0.021   0.002   TYR D 299 
 PHE   0.013   0.001   PHE D 689 
 TRP   0.009   0.001   TRP D 936 
 HIS   0.002   0.000   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6276)
  covalent geometry    : angle       0.72618 ( 8544)
  hydrogen bonds       : bond        0.04050 (  416)
  hydrogen bonds       : angle       5.83088 ( 1209)

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   27 MET cc_start: 0.7494 (ttm) cc_final: 0.6847 (tmm)
REVERT: D   92 MET cc_start: 0.8538 (mtt) cc_final: 0.8311 (mtt)
REVERT: D  368 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5020 (mm)
REVERT: D  417 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8749 (t0)
REVERT: D  790 ILE cc_start: 0.6460 (mm) cc_final: 0.6014 (mm)
REVERT: D  938 TRP cc_start: 0.6403 (m100) cc_final: 0.5810 (m100)
REVERT: I   17 GLU cc_start: 0.8665 (tp30) cc_final: 0.8458 (tp30)
REVERT: I   22 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7734 (mp)
REVERT: I   23 GLU cc_start: 0.8411 (mp0) cc_final: 0.8136 (mp0)
  outliers start: 21
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0615
  time to fit residues: 10.9972
Evaluate side-chains
  129 residues out of total 648 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  106 HIS
Chi-restraints excluded: chain D residue  113 ILE
Chi-restraints excluded: chain D residue  238 LEU
Chi-restraints excluded: chain D residue  368 LEU
Chi-restraints excluded: chain D residue  411 TYR
Chi-restraints excluded: chain D residue  417 ASP
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  795 THR
Chi-restraints excluded: chain D residue  798 VAL
Chi-restraints excluded: chain D residue  840 VAL
Chi-restraints excluded: chain D residue  862 ILE
Chi-restraints excluded: chain D residue  902 VAL
Chi-restraints excluded: chain D residue  933 LEU
Chi-restraints excluded: chain I residue   22 ILE
Chi-restraints excluded: chain I residue   28 THR
Chi-restraints excluded: chain I residue   31 LYS
Chi-restraints excluded: chain I residue   53 ASP
Chi-restraints excluded: chain I residue   78 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0770
   chunk 54 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7338

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.149820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.131030 restraints weight = 14125.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 3.40
r_work: 0.3892 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6276  Z= 0.168
  Angle     :  0.752  10.890   8544  Z= 0.372
  Chirality :  0.045   0.277   1028
  Planarity :  0.005   0.059   1082
  Dihedral  :  4.692  24.551    870
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 15.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.56 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.29 %
    Favored  : 77.31 %
  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: -0.50 (0.29), residues: 812
  helix:  0.24 (0.22), residues: 524
  sheet: -0.77 (0.85), residues: 40
  loop : -1.29 (0.41), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  99 
 TYR   0.015   0.002   TYR D 185 
 PHE   0.012   0.001   PHE D 689 
 TRP   0.007   0.001   TRP D 936 
 HIS   0.005   0.001   HIS D 308 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6276)
  covalent geometry    : angle       0.75216 ( 8544)
  hydrogen bonds       : bond        0.04305 (  416)
  hydrogen bonds       : angle       5.92264 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1348.12 seconds
wall clock time: 23 minutes 47.46 seconds (1427.46 seconds total)