Starting phenix.real_space_refine
on Tue Mar  3 16:34:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6u5h_20646/03_2026/6u5h_20646.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4530      2.51       5
     N    1362      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7326
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 2442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2442
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 304}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Restraints were copied for chains:
    B, A
  Time building chain proxies: 1.56, per 1000 atoms: 0.21
  Number of scatterers: 7326
  At special positions: 0
  Unit cell: (90.567, 94.731, 78.075, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1392      8.00
     N    1362      7.00
     C    4530      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 302.8 milliseconds
  

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 12 sheets defined
      10.1% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 155 through 160
      removed outlier: 3.754A  pdb=" N   ASP C 160 " --> pdb=" O   ALA C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 173 through 177
      removed outlier: 3.661A  pdb=" N   GLN C 176 " --> pdb=" O   LEU C 173 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER C 177 " --> pdb=" O   PRO C 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 173 through 177'
    Processing helix  chain 'C' and resid 252 through 256
      removed outlier: 3.609A  pdb=" N   GLU C 255 " --> pdb=" O   GLY C 252 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLN C 256 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 252 through 256'
    Processing helix  chain 'C' and resid 257 through 267
      removed outlier: 3.993A  pdb=" N   ARG C 261 " --> pdb=" O   ALA C 257 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA C 263 " --> pdb=" O   LYS C 259 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE C 265 " --> pdb=" O   ARG C 261 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER C 266 " --> pdb=" O   LEU C 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 17 through 21
    Processing helix  chain 'B' and resid 155 through 160
      removed outlier: 3.754A  pdb=" N   ASP B 160 " --> pdb=" O   ALA B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.661A  pdb=" N   GLN B 176 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER B 177 " --> pdb=" O   PRO B 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 173 through 177'
    Processing helix  chain 'B' and resid 252 through 256
      removed outlier: 3.609A  pdb=" N   GLU B 255 " --> pdb=" O   GLY B 252 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN B 256 " --> pdb=" O   GLU B 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 252 through 256'
    Processing helix  chain 'B' and resid 257 through 267
      removed outlier: 3.993A  pdb=" N   ARG B 261 " --> pdb=" O   ALA B 257 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE B 265 " --> pdb=" O   ARG B 261 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER B 266 " --> pdb=" O   LEU B 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 21
    Processing helix  chain 'A' and resid 155 through 160
      removed outlier: 3.753A  pdb=" N   ASP A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.661A  pdb=" N   GLN A 176 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   SER A 177 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 173 through 177'
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.610A  pdb=" N   GLU A 255 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 252 through 256'
    Processing helix  chain 'A' and resid 257 through 267
      removed outlier: 3.994A  pdb=" N   ARG A 261 " --> pdb=" O   ALA A 257 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 263 " --> pdb=" O   LYS A 259 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   PHE A 265 " --> pdb=" O   ARG A 261 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 8
      removed outlier: 3.668A  pdb=" N   GLY C  63 " --> pdb=" O   SER C   4 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   GLY C  73 " --> pdb=" O   VAL C  60 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU C  62 " --> pdb=" O   ARG C  71 " (cutoff:3.500A)
      removed outlier: 5.781A  pdb=" N   ARG C  71 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 22 through 26
      removed outlier: 6.357A  pdb=" N   ARG C  41 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LEU C  25 " --> pdb=" O   THR C  39 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   THR C  39 " --> pdb=" O   LEU C  25 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 190 through 191
      removed outlier: 5.676A  pdb=" N   ILE C 303 " --> pdb=" O   ASN C 322 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN C 322 " --> pdb=" O   ILE C 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 202 through 203
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8
      removed outlier: 3.667A  pdb=" N   GLY B  63 " --> pdb=" O   SER B   4 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLY B  73 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU B  62 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   ARG B  71 " --> pdb=" O   LEU B  62 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 26
      removed outlier: 6.357A  pdb=" N   ARG B  41 " --> pdb=" O   LEU B  23 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   LEU B  25 " --> pdb=" O   THR B  39 " (cutoff:3.500A)
      removed outlier: 6.053A  pdb=" N   THR B  39 " --> pdb=" O   LEU B  25 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 190 through 191
      removed outlier: 5.675A  pdb=" N   ILE B 303 " --> pdb=" O   ASN B 322 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN B 322 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 202 through 203
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 8
      removed outlier: 3.667A  pdb=" N   GLY A  63 " --> pdb=" O   SER A   4 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLY A  73 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   LEU A  62 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 5.782A  pdb=" N   ARG A  71 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 22 through 26
      removed outlier: 6.357A  pdb=" N   ARG A  41 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   LEU A  25 " --> pdb=" O   THR A  39 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   THR A  39 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 190 through 191
      removed outlier: 5.675A  pdb=" N   ILE A 303 " --> pdb=" O   ASN A 322 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ASN A 322 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 202 through 203

    81 hydrogen bonds defined for protein.
    225 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2539
        1.34 -     1.46: 1375
        1.46 -     1.58: 3460
        1.58 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 7443
  Sorted by residual:
  bond pdb=" C   LEU A 218 "
       pdb=" N   PRO A 219 "
    ideal  model  delta    sigma   weight residual
    1.341  1.362 -0.021 1.60e-02 3.91e+03 1.76e+00
  bond pdb=" CB  PRO A  86 "
       pdb=" CG  PRO A  86 "
    ideal  model  delta    sigma   weight residual
    1.492  1.426  0.066 5.00e-02 4.00e+02 1.76e+00
  bond pdb=" CB  PRO B  86 "
       pdb=" CG  PRO B  86 "
    ideal  model  delta    sigma   weight residual
    1.492  1.426  0.066 5.00e-02 4.00e+02 1.75e+00
  bond pdb=" CB  PRO C  86 "
       pdb=" CG  PRO C  86 "
    ideal  model  delta    sigma   weight residual
    1.492  1.426  0.066 5.00e-02 4.00e+02 1.75e+00
  bond pdb=" C   LEU B 218 "
       pdb=" N   PRO B 219 "
    ideal  model  delta    sigma   weight residual
    1.341  1.362 -0.021 1.60e-02 3.91e+03 1.66e+00
  ... (remaining 7438 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 9573
        2.10 -     4.20: 387
        4.20 -     6.30: 48
        6.30 -     8.39: 26
        8.39 -    10.49: 19
  Bond angle restraints: 10053
  Sorted by residual:
  angle pdb=" N   VAL B  14 "
        pdb=" CA  VAL B  14 "
        pdb=" C   VAL B  14 "
      ideal   model   delta    sigma   weight residual
     108.95  101.03    7.92 1.65e+00 3.67e-01 2.31e+01
  angle pdb=" N   VAL A  14 "
        pdb=" CA  VAL A  14 "
        pdb=" C   VAL A  14 "
      ideal   model   delta    sigma   weight residual
     108.95  101.07    7.88 1.65e+00 3.67e-01 2.28e+01
  angle pdb=" N   VAL C  14 "
        pdb=" CA  VAL C  14 "
        pdb=" C   VAL C  14 "
      ideal   model   delta    sigma   weight residual
     108.95  101.09    7.86 1.65e+00 3.67e-01 2.27e+01
  angle pdb=" CA  PRO A  85 "
        pdb=" C   PRO A  85 "
        pdb=" N   PRO A  86 "
      ideal   model   delta    sigma   weight residual
     117.93  123.03   -5.10 1.20e+00 6.94e-01 1.81e+01
  angle pdb=" CA  PRO B  85 "
        pdb=" C   PRO B  85 "
        pdb=" N   PRO B  86 "
      ideal   model   delta    sigma   weight residual
     117.93  123.00   -5.07 1.20e+00 6.94e-01 1.78e+01
  ... (remaining 10048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.28: 4254
       14.28 -    28.55: 249
       28.55 -    42.83: 9
       42.83 -    57.10: 0
       57.10 -    71.38: 6
  Dihedral angle restraints: 4518
    sinusoidal: 1830
      harmonic: 2688
  Sorted by residual:
  dihedral pdb=" CA  PHE B 199 "
           pdb=" C   PHE B 199 "
           pdb=" N   ASP B 200 "
           pdb=" CA  ASP B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.32   25.68     0      5.00e+00 4.00e-02 2.64e+01
  dihedral pdb=" CA  PHE A 199 "
           pdb=" C   PHE A 199 "
           pdb=" N   ASP A 200 "
           pdb=" CA  ASP A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.36   25.64     0      5.00e+00 4.00e-02 2.63e+01
  dihedral pdb=" CA  PHE C 199 "
           pdb=" C   PHE C 199 "
           pdb=" N   ASP C 200 "
           pdb=" CA  ASP C 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.37   25.63     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 4515 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 824
       0.058 -    0.117: 229
       0.117 -    0.175: 61
       0.175 -    0.233: 8
       0.233 -    0.292: 3
  Chirality restraints: 1125
  Sorted by residual:
  chirality pdb=" CB  ILE C 105 "
            pdb=" CA  ILE C 105 "
            pdb=" CG1 ILE C 105 "
            pdb=" CG2 ILE C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.94   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE A 105 "
            pdb=" CA  ILE A 105 "
            pdb=" CG1 ILE A 105 "
            pdb=" CG2 ILE A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.94   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE B 105 "
            pdb=" CA  ILE B 105 "
            pdb=" CG1 ILE B 105 "
            pdb=" CG2 ILE B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 1122 not shown)

  Planarity restraints: 1326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 187 "    0.041 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 188 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 187 "    0.041 5.00e-02 4.00e+02   6.30e-02 6.35e+00
        pdb=" N   PRO B 188 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO B 188 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 188 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 187 "    0.041 5.00e-02 4.00e+02   6.28e-02 6.32e+00
        pdb=" N   PRO C 188 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO C 188 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO C 188 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1323 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1109
        2.77 -     3.30: 6094
        3.30 -     3.83: 11304
        3.83 -     4.37: 13014
        4.37 -     4.90: 22207
  Nonbonded interactions: 53728
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  79 "
            pdb=" OG1 THR B  92 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG1 THR C  79 "
            pdb=" OG1 THR C  92 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG1 THR A  79 "
            pdb=" OG1 THR A  92 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" O   THR B 104 "
            pdb=" OG1 THR B 153 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   THR C 104 "
            pdb=" OG1 THR C 153 "
     model   vdw
     2.247 3.040
  ... (remaining 53723 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'B'
  selection = chain 'A'
}

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:             2.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.980
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
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   0.066   7443  Z= 0.241
  Angle     :  1.067  10.493  10053  Z= 0.571
  Chirality :  0.059   0.292   1125
  Planarity :  0.006   0.063   1326
  Dihedral  :  8.739  71.380   2796
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.59 %
    Favored  : 86.41 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  :  0.39 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.23 (0.22), residues: 942
  helix: -5.41 (0.09), residues: 90
  sheet: -3.34 (0.32), residues: 213
  loop : -3.43 (0.20), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 279 
 TYR   0.023   0.002   TYR C 310 
 PHE   0.011   0.002   PHE A 151 
 TRP   0.039   0.004   TRP B 315 
 HIS   0.006   0.002   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 7443)
  covalent geometry    : angle       1.06676 (10053)
  hydrogen bonds       : bond        0.29010 (   81)
  hydrogen bonds       : angle       8.41418 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 223
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   76 THR cc_start: 0.8442 (p) cc_final: 0.8184 (p)
REVERT: C  198 SER cc_start: 0.8614 (p) cc_final: 0.8386 (m)
REVERT: C  215 ARG cc_start: 0.6463 (mtt180) cc_final: 0.5761 (mmm160)
REVERT: B   44 ASP cc_start: 0.8156 (m-30) cc_final: 0.7889 (m-30)
REVERT: B   48 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7930 (mm-40)
REVERT: B   64 TYR cc_start: 0.8561 (m-10) cc_final: 0.8121 (m-10)
REVERT: B  215 ARG cc_start: 0.6355 (mtt180) cc_final: 0.5448 (mmm160)
REVERT: B  289 LEU cc_start: 0.7809 (mt) cc_final: 0.7508 (mt)
REVERT: A  205 ASP cc_start: 0.7634 (m-30) cc_final: 0.7286 (m-30)
REVERT: A  215 ARG cc_start: 0.6525 (mtt180) cc_final: 0.5844 (mmp-170)
REVERT: A  281 ASP cc_start: 0.7677 (m-30) cc_final: 0.7103 (m-30)
  outliers start: 3
  outliers final: 0
  residues processed: 226
  average time/residue: 0.1382
  time to fit residues: 38.1837
Evaluate side-chains
  135 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:   50.0000
   chunk 74 optimal weight:    0.3980
   overall best weight:    4.6788

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

Flipped N/Q/H residues before XYZ refinement:
C 242 HIS
B  81 GLN
B 242 HIS
A 242 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.225207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.186315 restraints weight = 8052.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.183211 restraints weight = 11479.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.183926 restraints weight = 9519.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.183057 restraints weight = 9469.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.183559 restraints weight = 7797.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6712
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   7443  Z= 0.204
  Angle     :  0.771   7.277  10053  Z= 0.395
  Chirality :  0.048   0.135   1125
  Planarity :  0.006   0.050   1326
  Dihedral  :  7.233  26.117   1059
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.72 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  :  8.11 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.09 (0.22), residues: 942
  helix: -5.09 (0.19), residues: 96
  sheet: -3.56 (0.26), residues: 267
  loop : -3.07 (0.22), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 286 
 TYR   0.021   0.002   TYR A 159 
 PHE   0.015   0.002   PHE C 265 
 TRP   0.027   0.003   TRP C 315 
 HIS   0.003   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7443)
  covalent geometry    : angle       0.77099 (10053)
  hydrogen bonds       : bond        0.03989 (   81)
  hydrogen bonds       : angle       5.84644 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  120 ARG cc_start: 0.7109 (mtt180) cc_final: 0.6851 (mmt90)
REVERT: C  205 ASP cc_start: 0.8003 (m-30) cc_final: 0.7653 (m-30)
REVERT: C  215 ARG cc_start: 0.6376 (mtt180) cc_final: 0.5887 (mmm160)
REVERT: C  322 ASN cc_start: 0.7202 (m110) cc_final: 0.6724 (m110)
REVERT: B  215 ARG cc_start: 0.6138 (mtt180) cc_final: 0.5565 (mmm160)
REVERT: B  302 LEU cc_start: 0.8523 (mt) cc_final: 0.8185 (mt)
REVERT: A  120 ARG cc_start: 0.6679 (mtt90) cc_final: 0.6173 (mmt90)
REVERT: A  205 ASP cc_start: 0.7827 (m-30) cc_final: 0.7379 (m-30)
REVERT: A  215 ARG cc_start: 0.6448 (mtt180) cc_final: 0.6010 (mmm160)
REVERT: A  259 LYS cc_start: 0.5969 (mttt) cc_final: 0.5644 (mmtp)
REVERT: A  322 ASN cc_start: 0.7097 (m110) cc_final: 0.6660 (m110)
  outliers start: 25
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1097
  time to fit residues: 23.7277
Evaluate side-chains
  150 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 16 optimal weight:    8.9990
   chunk 62 optimal weight:   20.0000
   chunk 82 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 56 optimal weight:   30.0000
   chunk 92 optimal weight:    7.9990
   chunk 34 optimal weight:    9.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 246 HIS
B 246 HIS
A 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.219033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.183719 restraints weight = 8050.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.181060 restraints weight = 12012.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.180756 restraints weight = 11175.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.179031 restraints weight = 10974.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.180118 restraints weight = 9010.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6793
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7443  Z= 0.228
  Angle     :  0.793   9.626  10053  Z= 0.404
  Chirality :  0.048   0.141   1125
  Planarity :  0.006   0.049   1326
  Dihedral  :  7.130  26.695   1059
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.48 %
    Favored  : 86.52 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 12.23 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.06 (0.23), residues: 942
  helix: -4.94 (0.22), residues: 114
  sheet: -3.49 (0.28), residues: 276
  loop : -2.98 (0.22), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 286 
 TYR   0.017   0.002   TYR B 159 
 PHE   0.023   0.002   PHE C 265 
 TRP   0.030   0.004   TRP C 315 
 HIS   0.004   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 7443)
  covalent geometry    : angle       0.79293 (10053)
  hydrogen bonds       : bond        0.03907 (   81)
  hydrogen bonds       : angle       5.43956 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  120 ARG cc_start: 0.7040 (mtt180) cc_final: 0.6791 (mmt90)
REVERT: C  209 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6482 (mtt)
REVERT: B  209 MET cc_start: 0.6673 (mtt) cc_final: 0.6391 (mtt)
REVERT: B  210 ARG cc_start: 0.6629 (mmt-90) cc_final: 0.6380 (mmt-90)
REVERT: B  289 LEU cc_start: 0.8197 (mt) cc_final: 0.7928 (mt)
REVERT: B  310 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6518 (m-10)
REVERT: A  173 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7828 (tp)
REVERT: A  205 ASP cc_start: 0.7934 (m-30) cc_final: 0.7254 (m-30)
REVERT: A  215 ARG cc_start: 0.6364 (mtt180) cc_final: 0.5844 (mmm160)
REVERT: A  322 ASN cc_start: 0.7109 (m110) cc_final: 0.6646 (m110)
  outliers start: 28
  outliers final: 21
  residues processed: 162
  average time/residue: 0.1160
  time to fit residues: 23.7368
Evaluate side-chains
  159 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  209 MET
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.3980
   chunk 43 optimal weight:   20.0000
   chunk 42 optimal weight:   20.0000
   chunk 87 optimal weight:   30.0000
   chunk 55 optimal weight:    0.9980
   chunk 88 optimal weight:    6.9990
   chunk 82 optimal weight:    6.9990
   chunk 58 optimal weight:    0.8980
   chunk 41 optimal weight:    9.9990
   overall best weight:    2.0182

-------------------------------------------------------------------------------
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 = 0.4383 r_free = 0.4383 target = 0.223472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.188419 restraints weight = 8151.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.186734 restraints weight = 13183.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.186496 restraints weight = 12059.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.185505 restraints weight = 10270.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.186054 restraints weight = 8974.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6673
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7443  Z= 0.128
  Angle     :  0.675   7.357  10053  Z= 0.340
  Chirality :  0.045   0.138   1125
  Planarity :  0.004   0.041   1326
  Dihedral  :  6.336  23.489   1059
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 14.54 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.93 (0.22), residues: 942
  helix: -4.96 (0.18), residues: 114
  sheet: -3.17 (0.27), residues: 300
  loop : -2.95 (0.22), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 286 
 TYR   0.008   0.001   TYR A 310 
 PHE   0.021   0.001   PHE A 265 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.003   0.001   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7443)
  covalent geometry    : angle       0.67498 (10053)
  hydrogen bonds       : bond        0.02781 (   81)
  hydrogen bonds       : angle       4.96692 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  120 ARG cc_start: 0.6928 (mtt180) cc_final: 0.6721 (mmt90)
REVERT: C  215 ARG cc_start: 0.6358 (mtt180) cc_final: 0.6030 (mmm160)
REVERT: B   78 ASP cc_start: 0.7744 (m-30) cc_final: 0.7452 (m-30)
REVERT: B  215 ARG cc_start: 0.6235 (mtt180) cc_final: 0.5726 (mmm160)
REVERT: B  310 TYR cc_start: 0.7455 (OUTLIER) cc_final: 0.6371 (m-10)
REVERT: A  205 ASP cc_start: 0.7801 (m-30) cc_final: 0.7228 (m-30)
REVERT: A  215 ARG cc_start: 0.6293 (mtt180) cc_final: 0.5900 (mmm160)
REVERT: A  322 ASN cc_start: 0.7136 (m110) cc_final: 0.6758 (m110)
  outliers start: 28
  outliers final: 21
  residues processed: 162
  average time/residue: 0.1153
  time to fit residues: 23.5844
Evaluate side-chains
  155 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  209 MET
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 19 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 45 optimal weight:   30.0000
   chunk 37 optimal weight:    7.9990
   chunk 72 optimal weight:   40.0000
   chunk 64 optimal weight:   10.0000
   chunk 34 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:   20.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN
C 179 GLN
B 179 GLN
A  81 GLN
A 179 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.213282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.179102 restraints weight = 8184.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.177708 restraints weight = 14442.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.178283 restraints weight = 11866.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.177406 restraints weight = 10353.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.177829 restraints weight = 9759.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.4651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   7443  Z= 0.275
  Angle     :  0.819  10.018  10053  Z= 0.415
  Chirality :  0.049   0.140   1125
  Planarity :  0.007   0.056   1326
  Dihedral  :  6.960  25.908   1059
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 17.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.45 %
    Favored  : 83.55 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 14.54 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.11 (0.23), residues: 942
  helix: -5.11 (0.16), residues: 114
  sheet: -3.44 (0.27), residues: 294
  loop : -2.98 (0.23), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 157 
 TYR   0.012   0.002   TYR B 159 
 PHE   0.026   0.002   PHE B 265 
 TRP   0.025   0.003   TRP A 315 
 HIS   0.004   0.001   HIS B 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 7443)
  covalent geometry    : angle       0.81852 (10053)
  hydrogen bonds       : bond        0.03455 (   81)
  hydrogen bonds       : angle       5.56304 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 134
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: C  294 LYS cc_start: 0.4586 (OUTLIER) cc_final: 0.4140 (mtmt)
REVERT: B  210 ARG cc_start: 0.5757 (mmt-90) cc_final: 0.4834 (mtt-85)
REVERT: B  289 LEU cc_start: 0.8416 (mt) cc_final: 0.8048 (mt)
REVERT: B  294 LYS cc_start: 0.5288 (OUTLIER) cc_final: 0.4718 (mtpt)
REVERT: B  322 ASN cc_start: 0.7292 (OUTLIER) cc_final: 0.6892 (m-40)
REVERT: A  215 ARG cc_start: 0.6234 (mtt180) cc_final: 0.5806 (mmm160)
  outliers start: 42
  outliers final: 28
  residues processed: 158
  average time/residue: 0.1270
  time to fit residues: 24.8047
Evaluate side-chains
  160 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  209 MET
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  294 LYS
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain B residue    4 SER
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  121 ASP
Chi-restraints excluded: chain B residue  198 SER
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  322 ASN
Chi-restraints excluded: chain A residue   14 VAL
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  121 ASP
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  272 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 10 optimal weight:   50.0000
   chunk 20 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0970
   chunk 13 optimal weight:    0.0370
   chunk 75 optimal weight:    0.0370
   chunk 70 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.4338

-------------------------------------------------------------------------------
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 = 0.4356 r_free = 0.4356 target = 0.221457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.186730 restraints weight = 8002.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.183668 restraints weight = 11932.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.182699 restraints weight = 11386.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.182229 restraints weight = 10171.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.182806 restraints weight = 9399.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.4798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7443  Z= 0.116
  Angle     :  0.681   8.011  10053  Z= 0.338
  Chirality :  0.046   0.179   1125
  Planarity :  0.004   0.038   1326
  Dihedral  :  6.162  23.136   1059
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.30 %
    Favored  : 89.70 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 17.37 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.77 (0.23), residues: 942
  helix: -4.86 (0.19), residues: 102
  sheet: -3.25 (0.26), residues: 303
  loop : -2.78 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 157 
 TYR   0.009   0.001   TYR B 216 
 PHE   0.015   0.001   PHE A 265 
 TRP   0.016   0.002   TRP A  82 
 HIS   0.002   0.001   HIS C 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 7443)
  covalent geometry    : angle       0.68069 (10053)
  hydrogen bonds       : bond        0.02436 (   81)
  hydrogen bonds       : angle       4.86279 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ARG cc_start: 0.7290 (mmt180) cc_final: 0.6869 (mpt180)
REVERT: B  169 MET cc_start: 0.3794 (mmt) cc_final: 0.3377 (mmt)
REVERT: B  209 MET cc_start: 0.6118 (OUTLIER) cc_final: 0.5808 (mtt)
REVERT: B  210 ARG cc_start: 0.5891 (mmt-90) cc_final: 0.5104 (tpp-160)
REVERT: B  294 LYS cc_start: 0.4817 (OUTLIER) cc_final: 0.4325 (mtpt)
REVERT: B  310 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6339 (m-10)
REVERT: A  215 ARG cc_start: 0.6227 (mtt180) cc_final: 0.5750 (mmm160)
REVERT: A  289 LEU cc_start: 0.8264 (mt) cc_final: 0.7823 (mt)
  outliers start: 28
  outliers final: 13
  residues processed: 146
  average time/residue: 0.1216
  time to fit residues: 22.3963
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  209 MET
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  209 MET
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  302 LEU
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 87 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 67 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    6.3988

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

Flipped N/Q/H residues before XYZ refinement:
B 322 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.213615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.182655 restraints weight = 8284.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.181277 restraints weight = 12557.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.179581 restraints weight = 13014.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.178170 restraints weight = 12784.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.178427 restraints weight = 10987.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.5130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7443  Z= 0.231
  Angle     :  0.755   7.994  10053  Z= 0.382
  Chirality :  0.047   0.166   1125
  Planarity :  0.006   0.045   1326
  Dihedral  :  6.639  25.393   1059
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.76 %
    Favored  : 85.24 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 16.60 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.00 (0.23), residues: 942
  helix: -4.97 (0.16), residues: 120
  sheet: -3.36 (0.27), residues: 294
  loop : -2.89 (0.23), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 157 
 TYR   0.013   0.002   TYR C 216 
 PHE   0.016   0.002   PHE A 265 
 TRP   0.019   0.002   TRP A 315 
 HIS   0.002   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 7443)
  covalent geometry    : angle       0.75547 (10053)
  hydrogen bonds       : bond        0.02972 (   81)
  hydrogen bonds       : angle       5.31975 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7199 (mpt180)
REVERT: B  169 MET cc_start: 0.3913 (mmt) cc_final: 0.3474 (mmt)
REVERT: B  199 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6642 (m-80)
REVERT: B  210 ARG cc_start: 0.6155 (mmt-90) cc_final: 0.4928 (mmt-90)
REVERT: B  294 LYS cc_start: 0.5008 (OUTLIER) cc_final: 0.4676 (mtmt)
REVERT: B  310 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6682 (m-10)
REVERT: A  215 ARG cc_start: 0.6296 (mtt180) cc_final: 0.5855 (mmm160)
REVERT: A  230 LYS cc_start: 0.3955 (mttt) cc_final: 0.3561 (tppp)
REVERT: A  322 ASN cc_start: 0.7116 (m110) cc_final: 0.6651 (m110)
  outliers start: 40
  outliers final: 25
  residues processed: 146
  average time/residue: 0.1336
  time to fit residues: 24.1439
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  198 SER
Chi-restraints excluded: chain C residue  199 PHE
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  272 VAL
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  321 CYS
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  204 ASP
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  294 LYS
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  272 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 76 optimal weight:    5.9990
   chunk 14 optimal weight:   40.0000
   chunk 9 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 3 optimal weight:    6.9990
   chunk 31 optimal weight:   10.0000
   chunk 69 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:   20.0000
   overall best weight:    3.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.216867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.183033 restraints weight = 8195.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.180499 restraints weight = 12304.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.179775 restraints weight = 11802.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.178926 restraints weight = 11235.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.179114 restraints weight = 8959.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3946
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.5244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7443  Z= 0.149
  Angle     :  0.699   7.828  10053  Z= 0.350
  Chirality :  0.046   0.166   1125
  Planarity :  0.005   0.038   1326
  Dihedral  :  6.250  24.140   1059
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.89 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.02 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.96 (0.23), residues: 942
  helix: -4.93 (0.17), residues: 120
  sheet: -3.28 (0.27), residues: 303
  loop : -2.88 (0.23), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 157 
 TYR   0.008   0.001   TYR C 159 
 PHE   0.016   0.001   PHE A 265 
 TRP   0.016   0.002   TRP A 315 
 HIS   0.002   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7443)
  covalent geometry    : angle       0.69896 (10053)
  hydrogen bonds       : bond        0.02480 (   81)
  hydrogen bonds       : angle       4.98329 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 ARG cc_start: 0.7407 (mmt180) cc_final: 0.7205 (mpt180)
REVERT: B  210 ARG cc_start: 0.6135 (mmt-90) cc_final: 0.5197 (mtt-85)
REVERT: B  310 TYR cc_start: 0.7547 (OUTLIER) cc_final: 0.6492 (m-10)
REVERT: A  215 ARG cc_start: 0.6315 (mtt180) cc_final: 0.5787 (mmm160)
REVERT: A  230 LYS cc_start: 0.3756 (mttt) cc_final: 0.3517 (tppp)
  outliers start: 30
  outliers final: 21
  residues processed: 140
  average time/residue: 0.1136
  time to fit residues: 19.8620
Evaluate side-chains
  139 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   39 THR
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  199 PHE
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  302 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  321 CYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  321 CYS
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 74 optimal weight:   30.0000
   chunk 79 optimal weight:    7.9990
   chunk 44 optimal weight:    0.1980
   chunk 60 optimal weight:   20.0000
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 6 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.4371 r_free = 0.4371 target = 0.222843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.188340 restraints weight = 8000.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.187136 restraints weight = 13750.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.187467 restraints weight = 12054.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.186420 restraints weight = 10919.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.186801 restraints weight = 9434.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7443  Z= 0.111
  Angle     :  0.660  10.117  10053  Z= 0.328
  Chirality :  0.045   0.162   1125
  Planarity :  0.004   0.038   1326
  Dihedral  :  5.822  21.007   1059
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 19.69 %
    Favored  : 77.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.65 (0.24), residues: 942
  helix: -4.86 (0.18), residues: 114
  sheet: -3.01 (0.27), residues: 306
  loop : -2.70 (0.24), residues: 522

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 157 
 TYR   0.006   0.001   TYR C 159 
 PHE   0.019   0.001   PHE B 293 
 TRP   0.010   0.001   TRP A 315 
 HIS   0.002   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 7443)
  covalent geometry    : angle       0.66012 (10053)
  hydrogen bonds       : bond        0.02326 (   81)
  hydrogen bonds       : angle       4.70545 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   23 LEU cc_start: 0.8512 (mt) cc_final: 0.8297 (mt)
REVERT: C  210 ARG cc_start: 0.6144 (mmt-90) cc_final: 0.5718 (tpp-160)
REVERT: B   53 ARG cc_start: 0.7276 (mtp-110) cc_final: 0.7052 (mtp85)
REVERT: B  120 ARG cc_start: 0.7340 (mmt180) cc_final: 0.7114 (mpt180)
REVERT: B  169 MET cc_start: 0.4033 (mmt) cc_final: 0.3555 (mmt)
REVERT: B  210 ARG cc_start: 0.5963 (mmt-90) cc_final: 0.5186 (mtt-85)
REVERT: B  310 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.6355 (m-10)
REVERT: A    1 MET cc_start: 0.7279 (mmp) cc_final: 0.7076 (mmp)
REVERT: A  289 LEU cc_start: 0.8075 (mt) cc_final: 0.7443 (mt)
  outliers start: 22
  outliers final: 18
  residues processed: 141
  average time/residue: 0.1142
  time to fit residues: 20.2311
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  321 CYS
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue   89 LEU
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 44 optimal weight:    8.9990
   chunk 92 optimal weight:    8.9990
   chunk 74 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 67 optimal weight:    9.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  81 GLN
B  81 GLN
A  81 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.213474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.179789 restraints weight = 8132.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.178413 restraints weight = 12157.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.174952 restraints weight = 13009.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.173676 restraints weight = 14666.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.174661 restraints weight = 11503.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.5566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7443  Z= 0.233
  Angle     :  0.759   9.434  10053  Z= 0.383
  Chirality :  0.048   0.157   1125
  Planarity :  0.006   0.075   1326
  Dihedral  :  6.543  24.710   1059
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 16.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.18 %
    Favored  : 84.82 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.82 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.10 (0.23), residues: 942
  helix: -4.64 (0.20), residues: 147
  sheet: -3.22 (0.29), residues: 288
  loop : -3.08 (0.24), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 157 
 TYR   0.011   0.002   TYR B 159 
 PHE   0.016   0.002   PHE C 199 
 TRP   0.018   0.002   TRP A 315 
 HIS   0.004   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 ( 7443)
  covalent geometry    : angle       0.75850 (10053)
  hydrogen bonds       : bond        0.02858 (   81)
  hydrogen bonds       : angle       5.34208 (  225)

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

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

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1884 Ramachandran restraints generated.
    942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   53 ARG cc_start: 0.7253 (mtp-110) cc_final: 0.6967 (mtp85)
REVERT: B  120 ARG cc_start: 0.7470 (mmt180) cc_final: 0.7225 (mpt180)
REVERT: B  310 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6747 (m-10)
REVERT: A  230 LYS cc_start: 0.3990 (mttt) cc_final: 0.3567 (tppp)
REVERT: A  289 LEU cc_start: 0.7996 (mt) cc_final: 0.7464 (mt)
  outliers start: 25
  outliers final: 21
  residues processed: 138
  average time/residue: 0.1274
  time to fit residues: 21.8444
Evaluate side-chains
  141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 SER
Chi-restraints excluded: chain C residue    7 ILE
Chi-restraints excluded: chain C residue   37 SER
Chi-restraints excluded: chain C residue   79 THR
Chi-restraints excluded: chain C residue  262 LEU
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  321 CYS
Chi-restraints excluded: chain B residue    7 ILE
Chi-restraints excluded: chain B residue   37 SER
Chi-restraints excluded: chain B residue   79 THR
Chi-restraints excluded: chain B residue  199 PHE
Chi-restraints excluded: chain B residue  229 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  310 TYR
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   37 SER
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  199 PHE
Chi-restraints excluded: chain A residue  209 MET
Chi-restraints excluded: chain A residue  262 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 36 optimal weight:    5.9990
   chunk 56 optimal weight:   30.0000
   chunk 62 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 13 optimal weight:    7.9990
   chunk 76 optimal weight:   40.0000
   chunk 15 optimal weight:    7.9990
   chunk 64 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   overall best weight:    6.5990

-------------------------------------------------------------------------------
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 = 0.4280 r_free = 0.4280 target = 0.212069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.177886 restraints weight = 8176.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.175366 restraints weight = 13011.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.174052 restraints weight = 12854.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.172700 restraints weight = 11918.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.172847 restraints weight = 10674.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.5756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7443  Z= 0.228
  Angle     :  0.758   9.995  10053  Z= 0.383
  Chirality :  0.048   0.164   1125
  Planarity :  0.006   0.062   1326
  Dihedral  :  6.708  25.441   1059
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 16.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.12 %
    Favored  : 85.88 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.18 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.18 (0.23), residues: 942
  helix: -4.61 (0.21), residues: 144
  sheet: -3.09 (0.28), residues: 306
  loop : -3.29 (0.23), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 157 
 TYR   0.009   0.001   TYR C 310 
 PHE   0.014   0.002   PHE C 199 
 TRP   0.021   0.002   TRP A 315 
 HIS   0.003   0.001   HIS C 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7443)
  covalent geometry    : angle       0.75838 (10053)
  hydrogen bonds       : bond        0.02782 (   81)
  hydrogen bonds       : angle       5.32001 (  225)

===============================================================================
Job complete
usr+sys time: 1225.52 seconds
wall clock time: 21 minutes 51.64 seconds (1311.64 seconds total)