Starting phenix.real_space_refine
on Fri Jun  6 05:14:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8huj_35041/06_2025/8huj_35041.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8huj_35041/06_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_35041/06_2025/8huj_35041.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8huj_35041/06_2025/8huj_35041.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8huj_35041/06_2025/8huj_35041.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8huj_35041/06_2025/8huj_35041.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.00, per 1000 atoms: 0.70
  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: 2.72
  Conformation dependent library (CDL) restraints added in 700.1 milliseconds
  

  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: 2.77
  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: 3.12

  Time building geometry restraints manager: 2.26 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:             0.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.370
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.220
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.032   0.003   PHE A  86 
 TYR   0.009   0.002   TYR A 170 
 ARG   0.007   0.001   ARG A 190 

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

*********************** 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  : 0.658 
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: 0.2272
  time to fit residues: 22.3716
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  : 0.708 
-------------------------------------------------------------------------------
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 59 optimal weight:    9.9990
   chunk 53 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0070
   chunk 35 optimal weight:   20.0000
   chunk 28 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   chunk 33 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    5.6006

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.102183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.069635 restraints weight = 21814.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.071782 restraints weight = 10860.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.073073 restraints weight = 7597.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1377

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= 0.221
  Angle     :  0.688  14.461  10527  Z= 0.346
  Chirality :  0.039   0.227   1275
  Planarity :  0.004   0.042    979
  Dihedral  : 21.928 164.363   2234
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 26.75 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.35), residues: 617
  helix:  0.63 (0.27), residues: 362
  sheet: -0.88 (0.60), residues: 68
  loop : -0.66 (0.51), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 
 PHE   0.040   0.003   PHE B 977 
 TYR   0.017   0.002   TYR A  48 
 ARG   0.006   0.001   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05803 (  362)
  hydrogen bonds       : angle       4.49340 (  938)
  covalent geometry    : bond        0.00480 ( 7457)
  covalent geometry    : angle       0.68806 (10527)

*********************** 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
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 MET cc_start: 0.5117 (mtm) cc_final: 0.4902 (mtm)
REVERT: A  187 MET cc_start: 0.6292 (tmm) cc_final: 0.5795 (ppp)
REVERT: A  228 MET cc_start: 0.4844 (tmm) cc_final: 0.4461 (tmm)
REVERT: A  293 HIS cc_start: 0.7901 (t-90) cc_final: 0.7657 (t-90)
REVERT: B  853 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.6910 (ptpt)
REVERT: B  890 ILE cc_start: 0.8786 (mm) cc_final: 0.8478 (mm)
REVERT: B  961 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8518 (tp-100)
  outliers start: 22
  outliers final: 13
  residues processed: 84
  average time/residue: 0.2072
  time to fit residues: 23.2506
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  : 0.705 
-------------------------------------------------------------------------------
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 45 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   chunk 9 optimal weight:   20.0000
   chunk 35 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 248 GLN
A 374 ASN
B 961 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.102894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.070273 restraints weight = 22233.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.072427 restraints weight = 10806.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.073718 restraints weight = 7480.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7457  Z= 0.184
  Angle     :  0.625  15.336  10527  Z= 0.312
  Chirality :  0.038   0.220   1275
  Planarity :  0.004   0.042    979
  Dihedral  : 21.782 162.623   2226
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 25.85 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.35), residues: 617
  helix:  0.91 (0.27), residues: 357
  sheet: -1.01 (0.61), residues: 68
  loop : -0.70 (0.50), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 287 
 HIS   0.003   0.001   HIS A 303 
 PHE   0.043   0.003   PHE B 977 
 TYR   0.014   0.002   TYR A  48 
 ARG   0.006   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05298 (  362)
  hydrogen bonds       : angle       4.13705 (  938)
  covalent geometry    : bond        0.00399 ( 7457)
  covalent geometry    : angle       0.62471 (10527)

*********************** 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: 28
    poor density    : 68
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.6498 (tmm) cc_final: 0.6003 (ppp)
REVERT: A  193 LYS cc_start: 0.4861 (OUTLIER) cc_final: 0.4660 (tptt)
REVERT: A  228 MET cc_start: 0.4789 (tmm) cc_final: 0.4338 (tmm)
REVERT: A  229 ARG cc_start: 0.6165 (ptp-170) cc_final: 0.5623 (mmp-170)
REVERT: A  293 HIS cc_start: 0.7832 (t-90) cc_final: 0.7609 (t-90)
REVERT: B  853 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6699 (ptpt)
REVERT: B  855 LYS cc_start: 0.7275 (mmtm) cc_final: 0.6873 (mttm)
REVERT: B  890 ILE cc_start: 0.8805 (mm) cc_final: 0.8511 (mm)
REVERT: B  986 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7031 (ttt-90)
  outliers start: 28
  outliers final: 15
  residues processed: 91
  average time/residue: 0.2197
  time to fit residues: 26.1246
Evaluate side-chains
  83 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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 16 optimal weight:   30.0000
   chunk 7 optimal weight:    0.0020
   chunk 55 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0050
   chunk 27 optimal weight:    0.2980
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   overall best weight:    1.6604

-------------------------------------------------------------------------------
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 = 0.3867 r_free = 0.3867 target = 0.105284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.072910 restraints weight = 22308.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.075313 restraints weight = 10779.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.076484 restraints weight = 7489.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.2268

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= 0.109
  Angle     :  0.533  13.533  10527  Z= 0.268
  Chirality :  0.036   0.181   1275
  Planarity :  0.003   0.040    979
  Dihedral  : 21.157 162.943   2222
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.83 %
    Favored  : 67.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.35), residues: 617
  helix:  1.35 (0.28), residues: 358
  sheet: -0.91 (0.61), residues: 66
  loop : -0.79 (0.48), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  27 
 HIS   0.002   0.001   HIS B 917 
 PHE   0.025   0.002   PHE B 977 
 TYR   0.007   0.001   TYR A 197 
 ARG   0.004   0.000   ARG A 255 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04067 (  362)
  hydrogen bonds       : angle       3.69979 (  938)
  covalent geometry    : bond        0.00229 ( 7457)
  covalent geometry    : angle       0.53270 (10527)

*********************** 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
  100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.2019 (ptt) cc_final: 0.0876 (mtm)
REVERT: A  161 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.7161 (mtp85)
REVERT: A  187 MET cc_start: 0.6594 (tmm) cc_final: 0.6238 (ppp)
REVERT: A  229 ARG cc_start: 0.6208 (ptp-170) cc_final: 0.5388 (mmp-170)
REVERT: A  293 HIS cc_start: 0.7809 (t-90) cc_final: 0.7591 (t-90)
REVERT: A  366 PHE cc_start: 0.3445 (OUTLIER) cc_final: 0.3195 (p90)
REVERT: B  780 MET cc_start: 0.7572 (mmm) cc_final: 0.7337 (mmm)
REVERT: B  791 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7863 (tt0)
REVERT: B  855 LYS cc_start: 0.7147 (mmtm) cc_final: 0.6733 (mttm)
REVERT: B  986 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7031 (ttt-90)
  outliers start: 24
  outliers final: 13
  residues processed: 95
  average time/residue: 0.2159
  time to fit residues: 27.1046
Evaluate side-chains
  84 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  260 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  366 PHE
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 34 optimal weight:   10.0000
   chunk 26 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9980
   chunk 48 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   overall best weight:    4.7988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.101890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.068680 restraints weight = 21425.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.070884 restraints weight = 10074.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.072265 restraints weight = 6832.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7457  Z= 0.189
  Angle     :  0.621  16.747  10527  Z= 0.310
  Chirality :  0.038   0.220   1275
  Planarity :  0.004   0.038    979
  Dihedral  : 21.422 161.522   2221
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 26.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.35), residues: 617
  helix:  1.30 (0.28), residues: 359
  sheet: -1.10 (0.60), residues: 68
  loop : -0.82 (0.49), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 
 PHE   0.026   0.002   PHE B 977 
 TYR   0.014   0.002   TYR A  48 
 ARG   0.004   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05183 (  362)
  hydrogen bonds       : angle       3.94907 (  938)
  covalent geometry    : bond        0.00409 ( 7457)
  covalent geometry    : angle       0.62145 (10527)

*********************** 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
  98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 67
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.6477 (tmm) cc_final: 0.6068 (ppp)
REVERT: A  258 TRP cc_start: 0.8408 (m-10) cc_final: 0.8137 (m-10)
REVERT: A  293 HIS cc_start: 0.7967 (t-90) cc_final: 0.7766 (t-90)
REVERT: B  776 PHE cc_start: 0.8016 (t80) cc_final: 0.7634 (t80)
REVERT: B  791 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8032 (tt0)
REVERT: B  855 LYS cc_start: 0.7069 (mmtm) cc_final: 0.6737 (mttm)
REVERT: B  977 PHE cc_start: 0.7912 (m-10) cc_final: 0.7691 (m-80)
REVERT: B  986 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6932 (ttt-90)
  outliers start: 31
  outliers final: 23
  residues processed: 91
  average time/residue: 0.1963
  time to fit residues: 24.3033
Evaluate side-chains
  92 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 LEU
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  314 ILE
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  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  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
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 44 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 61 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 63 optimal weight:   10.0000
   chunk 28 optimal weight:   20.0000
   overall best weight:    3.5988

-------------------------------------------------------------------------------
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 = 0.3802 r_free = 0.3802 target = 0.102487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.069328 restraints weight = 21440.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.071588 restraints weight = 10022.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.073010 restraints weight = 6743.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2514

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= 0.153
  Angle     :  0.582  16.556  10527  Z= 0.289
  Chirality :  0.037   0.204   1275
  Planarity :  0.003   0.039    979
  Dihedral  : 21.320 162.288   2221
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 27.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.35), residues: 617
  helix:  1.35 (0.28), residues: 359
  sheet: -1.21 (0.67), residues: 55
  loop : -0.85 (0.47), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 287 
 HIS   0.002   0.001   HIS A 303 
 PHE   0.022   0.002   PHE B 977 
 TYR   0.012   0.002   TYR A  48 
 ARG   0.004   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04759 (  362)
  hydrogen bonds       : angle       3.84663 (  938)
  covalent geometry    : bond        0.00330 ( 7457)
  covalent geometry    : angle       0.58209 (10527)

*********************** 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
  100 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 66
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  149 MET cc_start: 0.2085 (ptt) cc_final: 0.0789 (mtm)
REVERT: A  178 MET cc_start: 0.5150 (mtm) cc_final: 0.4785 (mtm)
REVERT: A  187 MET cc_start: 0.6460 (tmm) cc_final: 0.6088 (ppp)
REVERT: A  258 TRP cc_start: 0.8383 (m-10) cc_final: 0.8157 (m-10)
REVERT: A  291 LYS cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (mmmt)
REVERT: A  366 PHE cc_start: 0.3501 (OUTLIER) cc_final: 0.3256 (p90)
REVERT: B  776 PHE cc_start: 0.7961 (t80) cc_final: 0.7527 (t80)
REVERT: B  791 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8026 (tt0)
REVERT: B  855 LYS cc_start: 0.7144 (mmtm) cc_final: 0.6821 (mttm)
REVERT: B  977 PHE cc_start: 0.7922 (m-10) cc_final: 0.7695 (m-10)
REVERT: B  986 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6825 (ttt-90)
  outliers start: 34
  outliers final: 26
  residues processed: 93
  average time/residue: 0.2127
  time to fit residues: 26.8193
Evaluate side-chains
  96 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 66
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
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  291 LYS
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  299 VAL
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  314 ILE
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  836 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  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  981 ASP
Chi-restraints excluded: chain B residue  982 VAL
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 61 optimal weight:   10.0000
   chunk 41 optimal weight:    7.9990
   chunk 51 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 57 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 0 optimal weight:   50.0000
   chunk 68 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:   30.0000
   overall best weight:    6.7990

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.100975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.067967 restraints weight = 21483.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.070010 restraints weight = 10563.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.071290 restraints weight = 7338.357|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7457  Z= 0.251
  Angle     :  0.685  17.592  10527  Z= 0.340
  Chirality :  0.040   0.239   1275
  Planarity :  0.004   0.037    979
  Dihedral  : 21.644 162.219   2221
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 26.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.35), residues: 617
  helix:  0.98 (0.27), residues: 359
  sheet: -1.08 (0.67), residues: 56
  loop : -0.82 (0.49), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 287 
 HIS   0.004   0.001   HIS B 927 
 PHE   0.023   0.003   PHE B 977 
 TYR   0.019   0.002   TYR A  48 
 ARG   0.004   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05907 (  362)
  hydrogen bonds       : angle       4.15750 (  938)
  covalent geometry    : bond        0.00541 ( 7457)
  covalent geometry    : angle       0.68520 (10527)

*********************** 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
  104 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 65
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.7041 (mmm) cc_final: 0.6829 (mmm)
REVERT: A  178 MET cc_start: 0.5320 (mtm) cc_final: 0.5029 (mtm)
REVERT: A  187 MET cc_start: 0.6458 (tmm) cc_final: 0.6111 (ppp)
REVERT: B  791 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8034 (tt0)
REVERT: B  855 LYS cc_start: 0.7079 (mmtm) cc_final: 0.6764 (mttm)
REVERT: B  977 PHE cc_start: 0.7994 (m-10) cc_final: 0.7773 (m-10)
REVERT: B  986 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6900 (ttt-90)
  outliers start: 39
  outliers final: 31
  residues processed: 97
  average time/residue: 0.2335
  time to fit residues: 31.1371
Evaluate side-chains
  98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 65
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  230 ASP
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  302 MET
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  351 THR
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  836 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  962 MET
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 10 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 49 optimal weight:   20.0000
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:   30.0000
   chunk 34 optimal weight:    4.9990
   chunk 7 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3797 r_free = 0.3797 target = 0.102120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.069192 restraints weight = 21579.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.071341 restraints weight = 10506.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.072654 restraints weight = 7252.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7457  Z= 0.165
  Angle     :  0.597  16.623  10527  Z= 0.297
  Chirality :  0.037   0.207   1275
  Planarity :  0.003   0.039    979
  Dihedral  : 21.434 162.177   2221
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 27.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.35), residues: 617
  helix:  1.22 (0.28), residues: 359
  sheet: -1.17 (0.71), residues: 49
  loop : -0.93 (0.46), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 287 
 HIS   0.002   0.001   HIS A 303 
 PHE   0.028   0.002   PHE B 776 
 TYR   0.012   0.002   TYR A  48 
 ARG   0.003   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05017 (  362)
  hydrogen bonds       : angle       3.94198 (  938)
  covalent geometry    : bond        0.00356 ( 7457)
  covalent geometry    : angle       0.59724 (10527)

*********************** 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
  98 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 65
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.6994 (mmm) cc_final: 0.6785 (mmm)
REVERT: A  187 MET cc_start: 0.6542 (tmm) cc_final: 0.6171 (ppp)
REVERT: B  791 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7981 (tt0)
REVERT: B  855 LYS cc_start: 0.7090 (mmtm) cc_final: 0.6778 (mttm)
REVERT: B  977 PHE cc_start: 0.7987 (m-10) cc_final: 0.7774 (m-10)
REVERT: B  986 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6907 (ttt-90)
  outliers start: 33
  outliers final: 30
  residues processed: 91
  average time/residue: 0.3186
  time to fit residues: 38.8256
Evaluate side-chains
  97 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 LEU
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  299 VAL
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  351 THR
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  836 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 35 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.103806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.070727 restraints weight = 21571.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.073067 restraints weight = 9766.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.074528 restraints weight = 6471.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2953

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= 0.112
  Angle     :  0.546  15.757  10527  Z= 0.270
  Chirality :  0.036   0.181   1275
  Planarity :  0.003   0.042    979
  Dihedral  : 21.076 162.546   2221
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 28.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.35), residues: 617
  helix:  1.55 (0.28), residues: 360
  sheet: -1.13 (0.72), residues: 49
  loop : -1.02 (0.44), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 287 
 HIS   0.001   0.001   HIS A 303 
 PHE   0.016   0.002   PHE B 977 
 TYR   0.008   0.001   TYR A  48 
 ARG   0.002   0.000   ARG A 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04086 (  362)
  hydrogen bonds       : angle       3.67484 (  938)
  covalent geometry    : bond        0.00237 ( 7457)
  covalent geometry    : angle       0.54622 (10527)

*********************** 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
  95 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.7056 (mmm) cc_final: 0.6822 (mmm)
REVERT: A  143 GLU cc_start: 0.2486 (OUTLIER) cc_final: 0.2141 (mt-10)
REVERT: A  149 MET cc_start: 0.1764 (ptt) cc_final: 0.0576 (mtm)
REVERT: A  187 MET cc_start: 0.6515 (tmm) cc_final: 0.6147 (ppp)
REVERT: A  229 ARG cc_start: 0.6010 (ptt-90) cc_final: 0.5068 (mmp-170)
REVERT: A  366 PHE cc_start: 0.3468 (OUTLIER) cc_final: 0.3233 (p90)
REVERT: B  791 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7981 (tt0)
REVERT: B  855 LYS cc_start: 0.7107 (mmtm) cc_final: 0.6780 (mttm)
REVERT: B  977 PHE cc_start: 0.8067 (m-10) cc_final: 0.7825 (m-10)
REVERT: B  986 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.6932 (ttt-90)
  outliers start: 29
  outliers final: 24
  residues processed: 89
  average time/residue: 0.2242
  time to fit residues: 26.6895
Evaluate side-chains
  88 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 60
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  143 GLU
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 LEU
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  299 VAL
Chi-restraints excluded: chain A residue  302 MET
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  349 LEU
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  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  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 41 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 18 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 30 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9990
   chunk 66 optimal weight:   20.0000
   chunk 15 optimal weight:    7.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.102225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.069021 restraints weight = 21990.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071286 restraints weight = 10228.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072715 restraints weight = 6843.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7457  Z= 0.183
  Angle     :  0.615  15.993  10527  Z= 0.305
  Chirality :  0.038   0.215   1275
  Planarity :  0.003   0.040    979
  Dihedral  : 21.310 161.483   2221
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 28.90 %
    Favored  : 65.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.35), residues: 617
  helix:  1.32 (0.28), residues: 359
  sheet: -0.78 (0.71), residues: 55
  loop : -1.08 (0.46), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 
 PHE   0.031   0.003   PHE A  86 
 TYR   0.014   0.002   TYR A  48 
 ARG   0.003   0.000   ARG A 295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05083 (  362)
  hydrogen bonds       : angle       3.92843 (  938)
  covalent geometry    : bond        0.00394 ( 7457)
  covalent geometry    : angle       0.61468 (10527)

********************** 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
  90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 1.906 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 MET cc_start: 0.7084 (mmm) cc_final: 0.6871 (mmm)
REVERT: A  149 MET cc_start: 0.1785 (ptt) cc_final: 0.0740 (mtm)
REVERT: A  187 MET cc_start: 0.6548 (tmm) cc_final: 0.6169 (ppp)
REVERT: A  216 MET cc_start: 0.6048 (ptp) cc_final: 0.5717 (ptm)
REVERT: A  229 ARG cc_start: 0.6080 (ptt-90) cc_final: 0.5225 (mmp-170)
REVERT: A  366 PHE cc_start: 0.3512 (OUTLIER) cc_final: 0.3249 (p90)
REVERT: B  791 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8030 (tt0)
REVERT: B  855 LYS cc_start: 0.7123 (mmtm) cc_final: 0.6801 (mttm)
REVERT: B  977 PHE cc_start: 0.8047 (m-10) cc_final: 0.7804 (m-10)
REVERT: B  986 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6878 (ttt-90)
  outliers start: 30
  outliers final: 27
  residues processed: 83
  average time/residue: 0.4226
  time to fit residues: 48.5565
Evaluate side-chains
  90 residues out of total 557 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  211 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  302 MET
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  349 LEU
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  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  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  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 16 optimal weight:    5.9990
   chunk 62 optimal weight:   10.0000
   chunk 4 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 12 optimal weight:   30.0000
   chunk 53 optimal weight:    0.1980
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 9 optimal weight:   10.0000
   overall best weight:    4.2388

-------------------------------------------------------------------------------
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 = 0.3820 r_free = 0.3820 target = 0.102733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.070016 restraints weight = 21817.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.072198 restraints weight = 10705.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.073285 restraints weight = 7533.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.3033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7457  Z= 0.171
  Angle     :  0.600  15.822  10527  Z= 0.299
  Chirality :  0.038   0.209   1275
  Planarity :  0.003   0.039    979
  Dihedral  : 21.307 162.017   2221
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  6.46 %
    Allowed  : 27.83 %
    Favored  : 65.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.35), residues: 617
  helix:  1.25 (0.27), residues: 365
  sheet: -0.81 (0.71), residues: 55
  loop : -1.07 (0.47), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 287 
 HIS   0.003   0.001   HIS B 927 
 PHE   0.031   0.003   PHE A  86 
 TYR   0.013   0.002   TYR A 347 
 ARG   0.003   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05050 (  362)
  hydrogen bonds       : angle       3.91481 (  938)
  covalent geometry    : bond        0.00368 ( 7457)
  covalent geometry    : angle       0.60008 (10527)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3155.18 seconds
wall clock time: 58 minutes 31.55 seconds (3511.55 seconds total)