Starting phenix.real_space_refine
on Fri Aug 22 19:25:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8huj_35041/08_2025/8huj_35041.cif"
  }
  resolution = 3.76
  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=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      99      5.49       5
     Mg      3      5.21       5
     S      35      5.16       5
     C    4108      2.51       5
     N    1261      2.21       5
     O    1637      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7143
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3067
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 3067
          Classifications: {'peptide': 383}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 372}
    Chain: "B"
      Number of atoms: 1951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 238, 1951
          Classifications: {'peptide': 238}
          Link IDs: {'PTRANS': 5, 'TRANS': 232}
    Chain: "C"
      Number of atoms: 2121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2121
          Classifications: {'RNA': 99}
          Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 3, 'rna3p_pur': 44, 'rna3p_pyr': 41}
          Link IDs: {'rna2p': 14, 'rna3p': 84}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3, 'water': 1}
          Link IDs: {None: 3}
  Time building chain proxies: 1.73, per 1000 atoms: 0.24
  Number of scatterers: 7143
  At special positions: 0
  Unit cell: (100.98, 94.095, 119.34, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      35     16.00
     P      99     15.00
     Mg      3     11.99
     O    1637      8.00
     N    1261      7.00
     C    4108      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: 0.38
  Conformation dependent library (CDL) restraints added in 185.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1186

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 3 sheets defined
      65.1% alpha, 6.9% beta
      37 base pairs and 55 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 38
      removed outlier: 4.101A  pdb=" N   ASN A  38 " --> pdb=" O   ASP A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 40 through 51
    Processing helix  chain 'A' and resid 56 through 62
    Processing helix  chain 'A' and resid 63 through 69
      removed outlier: 3.564A  pdb=" N   GLY A  69 " --> pdb=" O   PRO A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 94
      removed outlier: 4.207A  pdb=" N   PHE A  86 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 123
    Processing helix  chain 'A' and resid 139 through 150
    Processing helix  chain 'A' and resid 158 through 167
    Processing helix  chain 'A' and resid 183 through 191
    Processing helix  chain 'A' and resid 192 through 203
    Processing helix  chain 'A' and resid 217 through 228
      removed outlier: 3.585A  pdb=" N   LYS A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 246
    Processing helix  chain 'A' and resid 257 through 269
      removed outlier: 4.416A  pdb=" N   ASP A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 295
      removed outlier: 3.570A  pdb=" N   ASP A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 321
    Processing helix  chain 'A' and resid 329 through 336
    Processing helix  chain 'A' and resid 354 through 361
      removed outlier: 3.926A  pdb=" N   HIS A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 365
      removed outlier: 3.555A  pdb=" N   ARG A 365 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 362 through 365'
    Processing helix  chain 'A' and resid 377 through 379
      No H-bonds generated for 'chain 'A' and resid 377 through 379'
    Processing helix  chain 'A' and resid 380 through 391
    Processing helix  chain 'A' and resid 401 through 406
      removed outlier: 4.310A  pdb=" N   LEU A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 755 through 771
    Processing helix  chain 'B' and resid 775 through 785
      removed outlier: 3.714A  pdb=" N   LEU B 779 " --> pdb=" O   MET B 775 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   LYS B 781 " --> pdb=" O   GLN B 777 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   GLN B 782 " --> pdb=" O   GLN B 778 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 790 through 808
    Processing helix  chain 'B' and resid 811 through 822
      removed outlier: 3.574A  pdb=" N   LEU B 822 " --> pdb=" O   MET B 818 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 838 through 852
    Processing helix  chain 'B' and resid 853 through 871
      removed outlier: 3.807A  pdb=" N   ASP B 858 " --> pdb=" O   ASP B 854 " (cutoff:3.500A)
      removed outlier: 5.125A  pdb=" N   GLU B 859 " --> pdb=" O   LYS B 855 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS B 866 " --> pdb=" O   GLU B 862 " (cutoff:3.500A)
      removed outlier: 4.979A  pdb=" N   GLU B 867 " --> pdb=" O   LYS B 863 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   MET B 868 " --> pdb=" O   LYS B 864 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ASP B 869 " --> pdb=" O   GLN B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 873 through 908
      removed outlier: 3.609A  pdb=" N   LEU B 908 " --> pdb=" O   GLU B 904 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 926
      removed outlier: 3.591A  pdb=" N   MET B 916 " --> pdb=" O   THR B 912 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL B 921 " --> pdb=" O   HIS B 917 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS B 922 " --> pdb=" O   ASP B 918 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 947
      removed outlier: 5.967A  pdb=" N   LYS B 944 " --> pdb=" O   THR B 940 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ASP B 945 " --> pdb=" O   THR B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 948 through 950
      No H-bonds generated for 'chain 'B' and resid 948 through 950'
    Processing helix  chain 'B' and resid 951 through 969
      removed outlier: 3.570A  pdb=" N   PHE B 959 " --> pdb=" O   MET B 955 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN B 960 " --> pdb=" O   ASP B 956 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 972 through 988
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133
      removed outlier: 6.462A  pdb=" N   HIS A 132 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A 104 " --> pdb=" O   VAL A 180 " (cutoff:3.500A)
      removed outlier: 7.766A  pdb=" N   ASP A 182 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   LEU A 106 " --> pdb=" O   ASP A 182 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   PHE A 179 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   LEU A 212 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A 181 " --> pdb=" O   LEU A 212 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   VAL A  72 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   SER A 213 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ALA A  74 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 301
      removed outlier: 6.490A  pdb=" N   SER A 300 " --> pdb=" O   ILE A 327 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   ALA A 275 " --> pdb=" O   LEU A 326 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   THR A 328 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   ILE A 277 " --> pdb=" O   THR A 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 827 through 828

    269 hydrogen bonds defined for protein.
    792 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      93 hydrogen bonds
      146 hydrogen bond angles
      0 basepair planarities
      37 basepair parallelities
      55 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 0.51 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: 1756
        1.33 -     1.46: 1895
        1.46 -     1.58: 3551
        1.58 -     1.70: 195
        1.70 -     1.82: 60
  Bond restraints: 7457
  Sorted by residual:
  bond pdb=" N   VAL B 835 "
       pdb=" CA  VAL B 835 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.038 1.32e-02 5.74e+03 8.07e+00
  bond pdb=" N   THR B 829 "
       pdb=" CA  THR B 829 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.23e-02 6.61e+03 6.87e+00
  bond pdb=" N   MET A 187 "
       pdb=" CA  MET A 187 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 6.79e+00
  bond pdb=" N   LYS A 369 "
       pdb=" CA  LYS A 369 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.19e-02 7.06e+03 6.73e+00
  bond pdb=" N   VAL A 180 "
       pdb=" CA  VAL A 180 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.19e-02 7.06e+03 6.41e+00
  ... (remaining 7452 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 10096
        1.97 -     3.93: 369
        3.93 -     5.90: 52
        5.90 -     7.87: 9
        7.87 -     9.83: 1
  Bond angle restraints: 10527
  Sorted by residual:
  angle pdb=" CA  PHE B 839 "
        pdb=" CB  PHE B 839 "
        pdb=" CG  PHE B 839 "
      ideal   model   delta    sigma   weight residual
     113.80  119.00   -5.20 1.00e+00 1.00e+00 2.70e+01
  angle pdb=" O3'   U C 778 "
        pdb=" C3'   U C 778 "
        pdb=" C2'   U C 778 "
      ideal   model   delta    sigma   weight residual
     113.70  121.48   -7.78 1.50e+00 4.44e-01 2.69e+01
  angle pdb=" N   ARG A 368 "
        pdb=" CA  ARG A 368 "
        pdb=" C   ARG A 368 "
      ideal   model   delta    sigma   weight residual
     111.28  106.15    5.13 1.09e+00 8.42e-01 2.22e+01
  angle pdb=" C4'   U C 778 "
        pdb=" C3'   U C 778 "
        pdb=" O3'   U C 778 "
      ideal   model   delta    sigma   weight residual
     113.00  119.98   -6.98 1.50e+00 4.44e-01 2.17e+01
  angle pdb=" CA  VAL B 835 "
        pdb=" C   VAL B 835 "
        pdb=" O   VAL B 835 "
      ideal   model   delta    sigma   weight residual
     121.92  117.02    4.90 1.17e+00 7.31e-01 1.75e+01
  ... (remaining 10522 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.18: 4196
       31.18 -    62.37: 405
       62.37 -    93.55: 108
       93.55 -   124.74: 2
      124.74 -   155.92: 1
  Dihedral angle restraints: 4712
    sinusoidal: 2893
      harmonic: 1819
  Sorted by residual:
  dihedral pdb=" C5'   A C 687 "
           pdb=" C4'   A C 687 "
           pdb=" C3'   A C 687 "
           pdb=" O3'   A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  108.10   38.90     1      8.00e+00 1.56e-02 3.33e+01
  dihedral pdb=" O4'   A C 687 "
           pdb=" C4'   A C 687 "
           pdb=" C3'   A C 687 "
           pdb=" C2'   A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00   -8.41   32.41     1      8.00e+00 1.56e-02 2.34e+01
  dihedral pdb=" O4'   A C 687 "
           pdb=" C1'   A C 687 "
           pdb=" N9    A C 687 "
           pdb=" C4    A C 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -172.85   66.85     1      1.70e+01 3.46e-03 2.02e+01
  ... (remaining 4709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.101: 1157
       0.101 -    0.202: 94
       0.202 -    0.302: 22
       0.302 -    0.403: 1
       0.403 -    0.504: 1
  Chirality restraints: 1275
  Sorted by residual:
  chirality pdb=" C3'   U C 778 "
            pdb=" C4'   U C 778 "
            pdb=" O3'   U C 778 "
            pdb=" C2'   U C 778 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.97   -0.50 2.00e-01 2.50e+01 6.35e+00
  chirality pdb=" C3'   A C 771 "
            pdb=" C4'   A C 771 "
            pdb=" O3'   A C 771 "
            pdb=" C2'   A C 771 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.78    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" P     G C 766 "
            pdb=" OP1   G C 766 "
            pdb=" OP2   G C 766 "
            pdb=" O5'   G C 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.69   -0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1272 not shown)

  Planarity restraints: 979
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 158 "   -0.014 2.00e-02 2.50e+03   2.74e-02 7.48e+00
        pdb=" C   THR A 158 "    0.047 2.00e-02 2.50e+03
        pdb=" O   THR A 158 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   PRO A 159 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  64 "    0.032 5.00e-02 4.00e+02   4.84e-02 3.74e+00
        pdb=" N   PRO A  65 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A  65 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A  65 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  86 "    0.013 2.00e-02 2.50e+03   1.39e-02 3.37e+00
        pdb=" CG  PHE A  86 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  86 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  86 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  86 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  86 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  86 "    0.002 2.00e-02 2.50e+03
  ... (remaining 976 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 829
        2.74 -     3.28: 7178
        3.28 -     3.82: 13651
        3.82 -     4.36: 15716
        4.36 -     4.90: 22689
  Nonbonded interactions: 60063
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 348 "
            pdb=" NH1 ARG A 359 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" O   CYS B 936 "
            pdb=" OG1 THR B 940 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" O   ILE A 246 "
            pdb=" NE2 GLN A 248 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" O2    C C 746 "
            pdb=" N6    A C 750 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" N   GLU A 379 "
            pdb=" OE1 GLU A 379 "
     model   vdw
     2.278 3.120
  ... (remaining 60058 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.670
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
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      :  0.005   0.038   7457  Z= 0.305
  Angle     :  0.828   9.832  10527  Z= 0.518
  Chirality :  0.062   0.504   1275
  Planarity :  0.004   0.048    979
  Dihedral  : 22.476 155.919   3526
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 26.21 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.39 (0.34), residues: 617
  helix:  0.44 (0.28), residues: 340
  sheet: -0.76 (0.64), residues: 61
  loop : -1.08 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 190 
 TYR   0.009   0.002   TYR A 170 
 PHE   0.032   0.003   PHE A  86 
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00496 ( 7457)
  covalent geometry    : angle       0.82765 (10527)
  hydrogen bonds       : bond        0.17853 (  362)
  hydrogen bonds       : angle       6.49450 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.5083 (mtm) cc_final: 0.4264 (mtm)
REVERT: A  228 MET cc_start: 0.4751 (tmm) cc_final: 0.4451 (tmm)
REVERT: B  845 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7996 (t0)
REVERT: B  890 ILE cc_start: 0.8839 (mm) cc_final: 0.8495 (mm)
  outliers start: 14
  outliers final: 5
  residues processed: 75
  average time/residue: 0.0938
  time to fit residues: 9.1808
Evaluate side-chains
  66 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  303 HIS
Chi-restraints excluded: chain A residue  368 ARG
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  845 ASN
Chi-restraints excluded: chain B residue  893 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
B 777 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.102819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.070029 restraints weight = 22177.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.072192 restraints weight = 10924.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.073483 restraints weight = 7607.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.074143 restraints weight = 6340.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.074420 restraints weight = 5817.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   7457  Z= 0.215
  Angle     :  0.680  14.381  10527  Z= 0.341
  Chirality :  0.039   0.220   1275
  Planarity :  0.004   0.042    979
  Dihedral  : 21.889 164.466   2234
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 26.03 %
    Favored  : 69.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.35), residues: 617
  helix:  0.70 (0.27), residues: 357
  sheet: -0.89 (0.60), residues: 68
  loop : -0.56 (0.51), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 362 
 TYR   0.017   0.002   TYR A  48 
 PHE   0.042   0.003   PHE B 977 
 TRP   0.012   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 7457)
  covalent geometry    : angle       0.67955 (10527)
  hydrogen bonds       : bond        0.05640 (  362)
  hydrogen bonds       : angle       4.41256 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.5139 (mtm) cc_final: 0.4898 (mtm)
REVERT: A  187 MET cc_start: 0.6277 (tmm) cc_final: 0.5761 (ppp)
REVERT: A  228 MET cc_start: 0.4724 (tmm) cc_final: 0.4287 (tmm)
REVERT: A  258 TRP cc_start: 0.8154 (m-10) cc_final: 0.7928 (m-10)
REVERT: A  293 HIS cc_start: 0.7872 (t-90) cc_final: 0.7635 (t-90)
REVERT: B  853 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.6871 (ptpt)
REVERT: B  855 LYS cc_start: 0.7390 (mmtm) cc_final: 0.6979 (mttm)
REVERT: B  890 ILE cc_start: 0.8783 (mm) cc_final: 0.8477 (mm)
REVERT: B  961 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8515 (tp-100)
  outliers start: 23
  outliers final: 13
  residues processed: 84
  average time/residue: 0.0840
  time to fit residues: 9.4877
Evaluate side-chains
  77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  829 THR
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  853 LYS
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  893 ARG
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  961 GLN
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:   40.0000
   chunk 44 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0870
   chunk 52 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:   40.0000
   chunk 58 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
A 248 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.104838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.072375 restraints weight = 22256.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.074730 restraints weight = 10809.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.075943 restraints weight = 7474.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076730 restraints weight = 6144.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.076658 restraints weight = 5636.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7457  Z= 0.118
  Angle     :  0.555  14.593  10527  Z= 0.277
  Chirality :  0.036   0.194   1275
  Planarity :  0.004   0.040    979
  Dihedral  : 21.430 162.845   2226
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 25.49 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.47 (0.35), residues: 617
  helix:  1.20 (0.28), residues: 358
  sheet: -1.05 (0.60), residues: 68
  loop : -0.73 (0.48), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 362 
 TYR   0.008   0.001   TYR A  48 
 PHE   0.033   0.002   PHE B 977 
 TRP   0.011   0.001   TRP A 287 
 HIS   0.002   0.001   HIS A 132 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7457)
  covalent geometry    : angle       0.55482 (10527)
  hydrogen bonds       : bond        0.04400 (  362)
  hydrogen bonds       : angle       3.89221 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.2224 (ptt) cc_final: 0.1138 (mtm)
REVERT: A  181 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7323 (tp)
REVERT: A  187 MET cc_start: 0.6525 (tmm) cc_final: 0.5999 (ppp)
REVERT: A  193 LYS cc_start: 0.4905 (OUTLIER) cc_final: 0.4692 (tptt)
REVERT: A  228 MET cc_start: 0.4741 (tmm) cc_final: 0.4469 (tmm)
REVERT: A  229 ARG cc_start: 0.6113 (ptp-170) cc_final: 0.5570 (mmp-170)
REVERT: A  293 HIS cc_start: 0.7804 (t-90) cc_final: 0.7577 (t-90)
REVERT: A  366 PHE cc_start: 0.3390 (OUTLIER) cc_final: 0.3179 (p90)
REVERT: B  853 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6908 (ptpt)
REVERT: B  855 LYS cc_start: 0.7253 (mmtm) cc_final: 0.6828 (mttm)
REVERT: B  863 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7791 (mtpt)
REVERT: B  890 ILE cc_start: 0.8739 (mm) cc_final: 0.8445 (mm)
REVERT: B  986 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6946 (ttt-90)
  outliers start: 23
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0950
  time to fit residues: 11.1350
Evaluate side-chains
  77 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  193 LYS
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  853 LYS
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 68 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 3 optimal weight:    8.9990
   chunk 36 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 65 optimal weight:   10.0000
   overall best weight:    8.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 960 ASN
B 961 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.100282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.067147 restraints weight = 22079.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.069280 restraints weight = 10827.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.070529 restraints weight = 7451.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.071181 restraints weight = 6199.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.071449 restraints weight = 5684.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   7457  Z= 0.312
  Angle     :  0.762  18.166  10527  Z= 0.381
  Chirality :  0.042   0.264   1275
  Planarity :  0.005   0.046    979
  Dihedral  : 21.867 162.440   2221
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 26.21 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.34), residues: 617
  helix:  0.62 (0.27), residues: 358
  sheet: -1.16 (0.60), residues: 68
  loop : -0.79 (0.50), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 362 
 TYR   0.023   0.003   TYR A  48 
 PHE   0.039   0.003   PHE B 977 
 TRP   0.018   0.003   TRP A  27 
 HIS   0.004   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00670 ( 7457)
  covalent geometry    : angle       0.76177 (10527)
  hydrogen bonds       : bond        0.06556 (  362)
  hydrogen bonds       : angle       4.39216 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 62
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.5348 (mtm) cc_final: 0.4504 (mtm)
REVERT: A  181 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7408 (tp)
REVERT: A  187 MET cc_start: 0.6453 (tmm) cc_final: 0.5944 (ppp)
REVERT: A  228 MET cc_start: 0.4737 (tmm) cc_final: 0.4444 (tmm)
REVERT: A  229 ARG cc_start: 0.6137 (ptp-170) cc_final: 0.5560 (mmp-170)
REVERT: A  258 TRP cc_start: 0.8548 (m-10) cc_final: 0.8308 (m-10)
REVERT: B  791 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8103 (tt0)
REVERT: B  863 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7922 (mtmt)
REVERT: B  986 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6928 (ttt-90)
  outliers start: 37
  outliers final: 22
  residues processed: 93
  average time/residue: 0.0851
  time to fit residues: 10.5888
Evaluate side-chains
  86 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 61
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 TRP
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  783 VAL
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  869 ASP
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  889 ASP
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0370
   chunk 67 optimal weight:   30.0000
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 36 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    1.4066

-------------------------------------------------------------------------------
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 = 0.3853 r_free = 0.3853 target = 0.104725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.072502 restraints weight = 22288.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.074890 restraints weight = 10810.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.076045 restraints weight = 7372.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.076898 restraints weight = 6129.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.076801 restraints weight = 5608.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7457  Z= 0.107
  Angle     :  0.547  16.444  10527  Z= 0.273
  Chirality :  0.036   0.175   1275
  Planarity :  0.003   0.041    979
  Dihedral  : 21.217 162.756   2221
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.01 %
    Favored  : 67.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.35), residues: 617
  helix:  1.25 (0.27), residues: 361
  sheet: -0.98 (0.65), residues: 60
  loop : -0.89 (0.47), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 161 
 TYR   0.006   0.001   TYR A  48 
 PHE   0.022   0.002   PHE B 977 
 TRP   0.021   0.002   TRP A  27 
 HIS   0.001   0.000   HIS B 917 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 7457)
  covalent geometry    : angle       0.54733 (10527)
  hydrogen bonds       : bond        0.04214 (  362)
  hydrogen bonds       : angle       3.73285 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.2060 (ptt) cc_final: 0.0809 (mtm)
REVERT: A  178 MET cc_start: 0.5367 (mtm) cc_final: 0.5047 (mtm)
REVERT: A  181 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7440 (tp)
REVERT: A  228 MET cc_start: 0.4710 (tmm) cc_final: 0.4455 (tmm)
REVERT: A  258 TRP cc_start: 0.8232 (m-10) cc_final: 0.8017 (m-10)
REVERT: A  366 PHE cc_start: 0.3401 (OUTLIER) cc_final: 0.3116 (p90)
REVERT: B  791 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7930 (tt0)
REVERT: B  855 LYS cc_start: 0.7045 (mmtm) cc_final: 0.6688 (mttm)
REVERT: B  977 PHE cc_start: 0.7836 (m-10) cc_final: 0.7607 (m-80)
REVERT: B  986 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6924 (ttt-90)
  outliers start: 25
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0958
  time to fit residues: 10.9314
Evaluate side-chains
  83 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  353 ARG
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 46 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 27 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 34 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
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 = 0.3824 r_free = 0.3824 target = 0.103781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.070899 restraints weight = 21626.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.073492 restraints weight = 10013.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.074500 restraints weight = 6578.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.075503 restraints weight = 5572.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.075359 restraints weight = 5018.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7457  Z= 0.110
  Angle     :  0.546  15.949  10527  Z= 0.271
  Chirality :  0.036   0.184   1275
  Planarity :  0.003   0.040    979
  Dihedral  : 21.109 162.152   2221
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 28.19 %
    Favored  : 67.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.35), residues: 617
  helix:  1.52 (0.28), residues: 359
  sheet: -0.84 (0.65), residues: 61
  loop : -0.84 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 161 
 TYR   0.009   0.001   TYR A  48 
 PHE   0.019   0.002   PHE B 977 
 TRP   0.010   0.002   TRP A 287 
 HIS   0.002   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 7457)
  covalent geometry    : angle       0.54647 (10527)
  hydrogen bonds       : bond        0.04066 (  362)
  hydrogen bonds       : angle       3.65819 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.1676 (ptt) cc_final: 0.0500 (mtm)
REVERT: A  178 MET cc_start: 0.5392 (mtm) cc_final: 0.5086 (mtm)
REVERT: A  181 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7345 (tp)
REVERT: A  187 MET cc_start: 0.6598 (tmm) cc_final: 0.6238 (tmm)
REVERT: A  229 ARG cc_start: 0.6028 (ptt-90) cc_final: 0.5302 (mmp-170)
REVERT: A  258 TRP cc_start: 0.8281 (m-10) cc_final: 0.8045 (m-10)
REVERT: A  366 PHE cc_start: 0.3532 (OUTLIER) cc_final: 0.3286 (p90)
REVERT: B  791 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7999 (tt0)
REVERT: B  855 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6811 (mttm)
REVERT: B  977 PHE cc_start: 0.7900 (m-10) cc_final: 0.7660 (m-10)
REVERT: B  986 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6986 (ttt-90)
  outliers start: 26
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0875
  time to fit residues: 10.0134
Evaluate side-chains
  82 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 61 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 1 optimal weight:    8.9990
   chunk 3 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    3.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.103941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.071387 restraints weight = 22175.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.073685 restraints weight = 10834.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.074926 restraints weight = 7557.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.075707 restraints weight = 6228.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.075617 restraints weight = 5679.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7457  Z= 0.157
  Angle     :  0.588  16.175  10527  Z= 0.292
  Chirality :  0.037   0.206   1275
  Planarity :  0.003   0.038    979
  Dihedral  : 21.241 161.492   2221
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 12.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 28.90 %
    Favored  : 66.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.35), residues: 617
  helix:  1.42 (0.28), residues: 359
  sheet: -0.76 (0.66), residues: 60
  loop : -0.84 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 877 
 TYR   0.011   0.002   TYR A  48 
 PHE   0.020   0.002   PHE B 977 
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 7457)
  covalent geometry    : angle       0.58815 (10527)
  hydrogen bonds       : bond        0.04733 (  362)
  hydrogen bonds       : angle       3.77760 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 60
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.1834 (ptt) cc_final: 0.0635 (mtm)
REVERT: A  178 MET cc_start: 0.5452 (mtm) cc_final: 0.5250 (mtm)
REVERT: A  181 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7277 (tp)
REVERT: A  187 MET cc_start: 0.6649 (tmm) cc_final: 0.6213 (tmm)
REVERT: A  258 TRP cc_start: 0.8338 (m-10) cc_final: 0.8121 (m-10)
REVERT: B  791 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7945 (tt0)
REVERT: B  855 LYS cc_start: 0.7184 (mmtm) cc_final: 0.6830 (mttm)
REVERT: B  977 PHE cc_start: 0.7981 (m-10) cc_final: 0.7732 (m-10)
REVERT: B  986 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7054 (ttt-90)
  outliers start: 25
  outliers final: 20
  residues processed: 80
  average time/residue: 0.0966
  time to fit residues: 10.2720
Evaluate side-chains
  82 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  353 ARG
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 5 optimal weight:    8.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3841 r_free = 0.3841 target = 0.104146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071780 restraints weight = 22321.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.074308 restraints weight = 10886.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.075183 restraints weight = 7408.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.075853 restraints weight = 6321.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.076088 restraints weight = 5862.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7457  Z= 0.140
  Angle     :  0.571  16.097  10527  Z= 0.282
  Chirality :  0.036   0.197   1275
  Planarity :  0.003   0.039    979
  Dihedral  : 21.176 162.370   2221
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 28.90 %
    Favored  : 66.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.35), residues: 617
  helix:  1.47 (0.28), residues: 359
  sheet: -0.58 (0.69), residues: 55
  loop : -0.88 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 877 
 TYR   0.010   0.001   TYR A  48 
 PHE   0.019   0.002   PHE B 977 
 TRP   0.011   0.002   TRP A 287 
 HIS   0.002   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7457)
  covalent geometry    : angle       0.57133 (10527)
  hydrogen bonds       : bond        0.04541 (  362)
  hydrogen bonds       : angle       3.70516 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 62
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.1924 (ptt) cc_final: 0.0857 (mtm)
REVERT: A  181 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7393 (tp)
REVERT: A  187 MET cc_start: 0.6593 (tmm) cc_final: 0.6160 (tmm)
REVERT: B  776 PHE cc_start: 0.7620 (t80) cc_final: 0.7261 (t80)
REVERT: B  791 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7979 (tt0)
REVERT: B  855 LYS cc_start: 0.7097 (mmtm) cc_final: 0.6766 (mttm)
REVERT: B  977 PHE cc_start: 0.8004 (m-10) cc_final: 0.7767 (m-10)
REVERT: B  986 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7092 (ttt-90)
  outliers start: 26
  outliers final: 23
  residues processed: 82
  average time/residue: 0.0871
  time to fit residues: 9.7653
Evaluate side-chains
  84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 58
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  353 ARG
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  836 THR
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 41 optimal weight:    9.9990
   chunk 64 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 59 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.104067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.071656 restraints weight = 21968.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.074188 restraints weight = 10768.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.075203 restraints weight = 7392.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.075851 restraints weight = 6216.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.076143 restraints weight = 5654.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7457  Z= 0.147
  Angle     :  0.583  16.129  10527  Z= 0.288
  Chirality :  0.036   0.203   1275
  Planarity :  0.003   0.039    979
  Dihedral  : 21.170 162.056   2221
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 28.37 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.35), residues: 617
  helix:  1.44 (0.28), residues: 359
  sheet: -0.70 (0.68), residues: 54
  loop : -0.90 (0.46), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 877 
 TYR   0.011   0.002   TYR A 267 
 PHE   0.031   0.002   PHE A  86 
 TRP   0.010   0.002   TRP A 287 
 HIS   0.002   0.001   HIS A 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 7457)
  covalent geometry    : angle       0.58318 (10527)
  hydrogen bonds       : bond        0.04669 (  362)
  hydrogen bonds       : angle       3.73067 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.1750 (ptt) cc_final: 0.0715 (mtm)
REVERT: A  181 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7325 (tt)
REVERT: A  187 MET cc_start: 0.6570 (tmm) cc_final: 0.6199 (tmm)
REVERT: A  258 TRP cc_start: 0.8119 (m-10) cc_final: 0.7897 (m-10)
REVERT: A  366 PHE cc_start: 0.3553 (OUTLIER) cc_final: 0.3320 (p90)
REVERT: B  791 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8000 (tt0)
REVERT: B  855 LYS cc_start: 0.7074 (mmtm) cc_final: 0.6741 (mttm)
REVERT: B  977 PHE cc_start: 0.8017 (m-10) cc_final: 0.7770 (m-10)
REVERT: B  986 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7117 (ttt-90)
  outliers start: 30
  outliers final: 25
  residues processed: 81
  average time/residue: 0.0918
  time to fit residues: 10.0652
Evaluate side-chains
  86 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  353 ARG
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  836 THR
Chi-restraints excluded: chain B residue  869 ASP
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  890 ILE
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 9 optimal weight:   20.0000
   chunk 13 optimal weight:    8.9990
   chunk 7 optimal weight:    0.3980
   chunk 65 optimal weight:   10.0000
   chunk 15 optimal weight:    9.9990
   chunk 53 optimal weight:    6.9990
   chunk 66 optimal weight:   20.0000
   chunk 26 optimal weight:    0.4980
   chunk 68 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   overall best weight:    4.7786

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.103158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.070681 restraints weight = 22189.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.073190 restraints weight = 10782.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.074096 restraints weight = 7382.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.074766 restraints weight = 6292.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.074810 restraints weight = 5798.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7457  Z= 0.188
  Angle     :  0.628  16.915  10527  Z= 0.310
  Chirality :  0.038   0.219   1275
  Planarity :  0.004   0.038    979
  Dihedral  : 21.324 162.126   2221
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 28.37 %
    Favored  : 66.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.35), residues: 617
  helix:  1.28 (0.27), residues: 359
  sheet: -0.63 (0.64), residues: 58
  loop : -0.89 (0.47), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 877 
 TYR   0.014   0.002   TYR A 267 
 PHE   0.033   0.003   PHE B 776 
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 7457)
  covalent geometry    : angle       0.62846 (10527)
  hydrogen bonds       : bond        0.05240 (  362)
  hydrogen bonds       : angle       3.88373 (  938)

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

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

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1234 Ramachandran restraints generated.
    617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 59
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.1903 (ptt) cc_final: 0.0788 (mtm)
REVERT: A  178 MET cc_start: 0.5468 (mtm) cc_final: 0.5008 (mtm)
REVERT: A  181 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7357 (tt)
REVERT: A  187 MET cc_start: 0.6555 (tmm) cc_final: 0.6197 (tmm)
REVERT: A  229 ARG cc_start: 0.5963 (ptt-90) cc_final: 0.4995 (mmp-170)
REVERT: A  366 PHE cc_start: 0.3529 (OUTLIER) cc_final: 0.3287 (p90)
REVERT: B  791 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7981 (tt0)
REVERT: B  855 LYS cc_start: 0.7082 (mmtm) cc_final: 0.6751 (mttm)
REVERT: B  977 PHE cc_start: 0.8043 (m-10) cc_final: 0.7792 (m-10)
REVERT: B  986 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7044 (ttt-90)
  outliers start: 30
  outliers final: 25
  residues processed: 82
  average time/residue: 0.0830
  time to fit residues: 9.2053
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 59
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  353 ARG
Chi-restraints excluded: chain A residue  366 PHE
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain B residue  772 THR
Chi-restraints excluded: chain B residue  791 GLU
Chi-restraints excluded: chain B residue  798 ILE
Chi-restraints excluded: chain B residue  827 VAL
Chi-restraints excluded: chain B residue  834 THR
Chi-restraints excluded: chain B residue  836 THR
Chi-restraints excluded: chain B residue  869 ASP
Chi-restraints excluded: chain B residue  884 LEU
Chi-restraints excluded: chain B residue  899 ILE
Chi-restraints excluded: chain B residue  918 ASP
Chi-restraints excluded: chain B residue  936 CYS
Chi-restraints excluded: chain B residue  962 MET
Chi-restraints excluded: chain B residue  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
Chi-restraints excluded: chain B residue  986 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0470
   chunk 58 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 68 optimal weight:   20.0000
   chunk 48 optimal weight:   30.0000
   chunk 13 optimal weight:   20.0000
   chunk 50 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0970
   overall best weight:    0.5878

-------------------------------------------------------------------------------
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 = 0.3876 r_free = 0.3876 target = 0.105761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.073445 restraints weight = 21920.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.075727 restraints weight = 10621.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.076900 restraints weight = 7414.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.077758 restraints weight = 6050.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.077646 restraints weight = 5571.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.3317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7457  Z= 0.097
  Angle     :  0.537  15.187  10527  Z= 0.264
  Chirality :  0.035   0.169   1275
  Planarity :  0.003   0.041    979
  Dihedral  : 20.738 163.095   2221
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 30.16 %
    Favored  : 66.07 %
  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 aren not related in a simple way.
  whole:  0.92 (0.35), residues: 617
  helix:  1.65 (0.28), residues: 360
  sheet: -0.43 (0.68), residues: 53
  loop : -0.98 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 877 
 TYR   0.008   0.001   TYR B 815 
 PHE   0.028   0.002   PHE A  86 
 TRP   0.027   0.003   TRP A  27 
 HIS   0.001   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 7457)
  covalent geometry    : angle       0.53724 (10527)
  hydrogen bonds       : bond        0.03745 (  362)
  hydrogen bonds       : angle       3.50017 (  938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1263.04 seconds
wall clock time: 22 minutes 25.47 seconds (1345.47 seconds total)