Starting phenix.real_space_refine
on Thu Jul  2 00:33:23 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vhg_43237/07_2026/8vhg_43237.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      36      5.49       5
     S      28      5.16       5
     C    2880      2.51       5
     N     844      2.21       5
     O     931      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-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4719
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2271
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 286, 2271
          Classifications: {'peptide': 286}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 9, 'TRANS': 276}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 1710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1710
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 43}
          Link IDs: {'PTRANS': 4, 'TRANS': 221}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 194
          Unresolved non-hydrogen dihedrals: 125
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'TYR:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 90
    Chain: "C"
      Number of atoms: 366
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 366
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
    Chain: "D"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 372
          Classifications: {'DNA': 18}
          Link IDs: {'rna3p': 17}
  Time building chain proxies: 1.21, per 1000 atoms: 0.26
  Number of scatterers: 4719
  At special positions: 0
  Unit cell: (113.22, 106.08, 86.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      36     15.00
     O     931      8.00
     N     844      7.00
     C    2880      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: 0.36
  Conformation dependent library (CDL) restraints added in 113.2 milliseconds
  

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  986

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 5 sheets defined
      35.2% alpha, 12.7% beta
      17 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 40
      removed outlier: 4.048A  pdb=" N   LYS A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   GLU A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 69
      removed outlier: 3.756A  pdb=" N   ILE A  56 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   MET A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ARG A  58 " --> pdb=" O   ALA A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.835A  pdb=" N   SER A 116 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   PHE A 118 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 4.283A  pdb=" N   THR A 127 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.877A  pdb=" N   THR A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 265
      removed outlier: 4.270A  pdb=" N   LEU A 264 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 299
      removed outlier: 4.447A  pdb=" N   GLU A 287 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 4.476A  pdb=" N   LYS A 291 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 99
      removed outlier: 4.014A  pdb=" N   LEU B  95 " --> pdb=" O   PHE B  91 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ALA B  96 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   SER B  97 " --> pdb=" O   ASP B  93 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 124
      removed outlier: 3.904A  pdb=" N   LYS B 123 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   THR B 124 " --> pdb=" O   GLN B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 155
      removed outlier: 5.101A  pdb=" N   ARG B 153 " --> pdb=" O   HIS B 149 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA B 155 " --> pdb=" O   ILE B 151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 3.532A  pdb=" N   LEU B 196 " --> pdb=" O   PHE B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 207
    Processing helix  chain 'B' and resid 356 through 361
    Processing helix  chain 'B' and resid 372 through 377
      removed outlier: 4.490A  pdb=" N   TYR B 376 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   PHE B 377 " --> pdb=" O   CYS B 373 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 372 through 377'
    Processing helix  chain 'B' and resid 381 through 394
      removed outlier: 3.681A  pdb=" N   LEU B 385 " --> pdb=" O   ASP B 381 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLN B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 7.108A  pdb=" N   VAL A 101 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   LEU A 111 " --> pdb=" O   ILE A  99 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   ILE A  99 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A  98 " --> pdb=" O   CYS A 226 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLN A 198 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS A 195 " --> pdb=" O   PHE A 168 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 168 " --> pdb=" O   CYS A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 257
      removed outlier: 4.071A  pdb=" N   SER A 246 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   CYS A 339 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   ILE A 337 " --> pdb=" O   HIS A 248 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   MET A 338 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A 340 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   GLN A 322 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL A 302 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310
      removed outlier: 3.909A  pdb=" N   TYR A 307 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A 317 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172
      removed outlier: 4.510A  pdb=" N   PHE B 171 " --> pdb=" O   VAL B 161 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   PHE B 160 " --> pdb=" O   ALA B 316 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA B 316 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 424
      removed outlier: 3.598A  pdb=" N   PHE B 421 " --> pdb=" O   VAL B 435 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 435 " --> pdb=" O   PHE B 421 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TYR B 433 " --> pdb=" O   PHE B 423 " (cutoff:3.500A)

    127 hydrogen bonds defined for protein.
    357 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      46 hydrogen bonds
      92 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1393
        1.34 -     1.46: 1333
        1.46 -     1.58: 2039
        1.58 -     1.71: 69
        1.71 -     1.83: 44
  Bond restraints: 4878
  Sorted by residual:
  bond pdb=" C3'  DG D   3 "
       pdb=" C2'  DG D   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.14e+01
  bond pdb=" C3'  DC C  17 "
       pdb=" C2'  DC C  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  bond pdb=" C5'  DG C  12 "
       pdb=" C4'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.512  1.489  0.023 7.00e-03 2.04e+04 1.04e+01
  bond pdb=" N9   DG D  17 "
       pdb=" C4   DG D  17 "
    ideal  model  delta    sigma   weight residual
    1.375  1.399 -0.024 8.00e-03 1.56e+04 9.24e+00
  bond pdb=" P    DG C  12 "
       pdb=" O5'  DG C  12 "
    ideal  model  delta    sigma   weight residual
    1.593  1.564  0.029 1.00e-02 1.00e+04 8.20e+00
  ... (remaining 4873 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 6476
        1.80 -     3.61: 215
        3.61 -     5.41: 26
        5.41 -     7.21: 8
        7.21 -     9.02: 2
  Bond angle restraints: 6727
  Sorted by residual:
  angle pdb=" N3   DT D  19 "
        pdb=" C4   DT D  19 "
        pdb=" O4   DT D  19 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.09e+01
  angle pdb=" O5'  DG C  12 "
        pdb=" C5'  DG C  12 "
        pdb=" C4'  DG C  12 "
      ideal   model   delta    sigma   weight residual
     109.40  105.93    3.47 8.00e-01 1.56e+00 1.88e+01
  angle pdb=" N3   DT D  13 "
        pdb=" C4   DT D  13 "
        pdb=" O4   DT D  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT C  13 "
        pdb=" C4   DT C  13 "
        pdb=" O4   DT C  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.31   -2.41 6.00e-01 2.78e+00 1.62e+01
  angle pdb=" N3   DT D   5 "
        pdb=" C4   DT D   5 "
        pdb=" O4   DT D   5 "
      ideal   model   delta    sigma   weight residual
     119.90  122.29   -2.39 6.00e-01 2.78e+00 1.58e+01
  ... (remaining 6722 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 2278
       17.32 -    34.64: 325
       34.64 -    51.96: 149
       51.96 -    69.28: 52
       69.28 -    86.59: 2
  Dihedral angle restraints: 2806
    sinusoidal: 1307
      harmonic: 1499
  Sorted by residual:
  dihedral pdb=" CA  THR B 401 "
           pdb=" C   THR B 401 "
           pdb=" N   ASN B 402 "
           pdb=" CA  ASN B 402 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.18   22.82     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN B 402 "
           pdb=" C   ASN B 402 "
           pdb=" N   CYS B 403 "
           pdb=" CA  CYS B 403 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.20  -19.80     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  SER B 418 "
           pdb=" C   SER B 418 "
           pdb=" N   ARG B 419 "
           pdb=" CA  ARG B 419 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.97   19.03     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 2803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 462
       0.035 -    0.069: 204
       0.069 -    0.104: 75
       0.104 -    0.139: 26
       0.139 -    0.174: 3
  Chirality restraints: 770
  Sorted by residual:
  chirality pdb=" CG  LEU A 222 "
            pdb=" CB  LEU A 222 "
            pdb=" CD1 LEU A 222 "
            pdb=" CD2 LEU A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.53e-01
  chirality pdb=" CA  VAL A 199 "
            pdb=" N   VAL A 199 "
            pdb=" C   VAL A 199 "
            pdb=" CB  VAL A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.43e-01
  chirality pdb=" CB  VAL A 199 "
            pdb=" CA  VAL A 199 "
            pdb=" CG1 VAL A 199 "
            pdb=" CG2 VAL A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 767 not shown)

  Planarity restraints: 720
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 425 "    0.033 5.00e-02 4.00e+02   4.99e-02 3.99e+00
        pdb=" N   PRO B 426 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 426 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 426 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  24 "   -0.168 9.50e-02 1.11e+02   7.52e-02 3.52e+00
        pdb=" NE  ARG A  24 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  24 "    0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  24 "    0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  24 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 268 "    0.030 5.00e-02 4.00e+02   4.59e-02 3.37e+00
        pdb=" N   PRO A 269 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 269 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 269 "    0.026 5.00e-02 4.00e+02
  ... (remaining 717 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1274
        2.82 -     3.34: 4296
        3.34 -     3.86: 7422
        3.86 -     4.38: 8100
        4.38 -     4.90: 12698
  Nonbonded interactions: 33790
  Sorted by model distance:
  nonbonded pdb=" O5'  DG C  12 "
            pdb=" O4'  DG C  12 "
     model   vdw
     2.303 2.432
  nonbonded pdb=" O5'  DC D   4 "
            pdb=" O4'  DC D   4 "
     model   vdw
     2.502 2.432
  nonbonded pdb=" O5'  DG C   3 "
            pdb=" O4'  DG C   3 "
     model   vdw
     2.511 2.432
  nonbonded pdb=" O5'  DT C  13 "
            pdb=" O4'  DT C  13 "
     model   vdw
     2.538 2.432
  nonbonded pdb=" O5'  DG C  16 "
            pdb=" O4'  DG C  16 "
     model   vdw
     2.546 2.432
  ... (remaining 33785 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.230
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6552
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   0.057   4878  Z= 0.381
  Angle     :  0.773   9.017   6727  Z= 0.527
  Chirality :  0.046   0.174    770
  Planarity :  0.007   0.075    720
  Dihedral  : 20.382  86.594   1820
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  :  4.12 %
    Favored  : 93.22 %
  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: -2.84 (0.37), residues: 482
  helix: -0.58 (0.43), residues: 140
  sheet: -2.41 (0.47), residues: 99
  loop : -2.45 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  15 
 TYR   0.016   0.002   TYR B 287 
 PHE   0.014   0.002   PHE B 171 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.006   0.001   HIS A 268 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00486 /  0.38 ( 4878)
  covalent geometry    : angle       0.77304 /  0.53 ( 6727)
  hydrogen bonds       : bond        0.17228 / 12.29 (  173)
  hydrogen bonds       : angle       7.31331 /  5.13 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 VAL cc_start: 0.6726 (m) cc_final: 0.6490 (t)
REVERT: A  191 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6220 (mttt)
REVERT: A  256 TYR cc_start: 0.6646 (t80) cc_final: 0.5887 (t80)
REVERT: A  273 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6249 (mm)
REVERT: A  287 GLU cc_start: 0.8028 (pp20) cc_final: 0.7628 (pp20)
REVERT: B   91 PHE cc_start: 0.6909 (m-80) cc_final: 0.6509 (m-10)
REVERT: B  184 GLN cc_start: 0.7629 (mm-40) cc_final: 0.6451 (pt0)
REVERT: B  338 MET cc_start: 0.7024 (tpp) cc_final: 0.6601 (mmm)
  outliers start: 11
  outliers final: 6
  residues processed: 125
  average time/residue: 0.0896
  time to fit residues: 13.5304
Evaluate side-chains
  118 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 GLU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain B residue  343 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5978

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.112457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.103190 restraints weight = 16502.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.105059 restraints weight = 9704.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.106301 restraints weight = 6264.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.107160 restraints weight = 4352.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.107789 restraints weight = 3201.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6555
moved from start:          0.1072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4878  Z= 0.171
  Angle     :  0.671   7.595   6727  Z= 0.377
  Chirality :  0.044   0.187    770
  Planarity :  0.005   0.043    720
  Dihedral  : 22.307  85.777    939
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.47 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 12.11 %
    Favored  : 82.32 %
  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: -2.49 (0.38), residues: 482
  helix: -0.28 (0.43), residues: 141
  sheet: -2.21 (0.49), residues: 99
  loop : -2.24 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 245 
 TYR   0.012   0.001   TYR A  35 
 PHE   0.012   0.002   PHE A 244 
 TRP   0.005   0.002   TRP B 420 
 HIS   0.012   0.001   HIS A 136 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00346 /  0.17 ( 4878)
  covalent geometry    : angle       0.67090 /  0.38 ( 6727)
  hydrogen bonds       : bond        0.07069 /  4.89 (  173)
  hydrogen bonds       : angle       5.79447 /  4.12 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7474 (pp)
REVERT: A   47 VAL cc_start: 0.6707 (m) cc_final: 0.6490 (t)
REVERT: A  191 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6227 (mttt)
REVERT: A  256 TYR cc_start: 0.6402 (t80) cc_final: 0.5729 (t80)
REVERT: A  268 HIS cc_start: 0.5352 (t70) cc_final: 0.5100 (t70)
REVERT: A  271 GLU cc_start: 0.6207 (pt0) cc_final: 0.6004 (tp30)
REVERT: A  273 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5809 (mm)
REVERT: A  287 GLU cc_start: 0.8021 (pp20) cc_final: 0.7614 (pp20)
REVERT: B   83 ARG cc_start: 0.7397 (mtm110) cc_final: 0.7160 (mtm110)
REVERT: B   87 LYS cc_start: 0.7918 (mmmm) cc_final: 0.7109 (pttt)
REVERT: B  184 GLN cc_start: 0.7638 (mm-40) cc_final: 0.6455 (pt0)
REVERT: B  338 MET cc_start: 0.6968 (tpp) cc_final: 0.6556 (mmm)
  outliers start: 23
  outliers final: 12
  residues processed: 126
  average time/residue: 0.0946
  time to fit residues: 14.3957
Evaluate side-chains
  122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 21 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0970
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.4978

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.112948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.103563 restraints weight = 16489.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.105458 restraints weight = 9589.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.106729 restraints weight = 6164.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.107580 restraints weight = 4270.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.108215 restraints weight = 3149.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4878  Z= 0.152
  Angle     :  0.643   6.676   6727  Z= 0.359
  Chirality :  0.043   0.164    770
  Planarity :  0.004   0.039    720
  Dihedral  : 22.140  81.258    934
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 16.95 %
    Favored  : 78.45 %
  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: -2.31 (0.38), residues: 482
  helix: -0.01 (0.44), residues: 141
  sheet: -2.04 (0.50), residues: 99
  loop : -2.26 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.007   0.001   TYR A 307 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.004   0.001   TRP A 318 
 HIS   0.007   0.001   HIS A 136 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.15 ( 4878)
  covalent geometry    : angle       0.64295 /  0.36 ( 6727)
  hydrogen bonds       : bond        0.06168 /  4.29 (  173)
  hydrogen bonds       : angle       5.42858 /  3.89 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7298 (pp)
REVERT: A   35 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.7511 (t80)
REVERT: A   47 VAL cc_start: 0.6677 (m) cc_final: 0.6456 (t)
REVERT: A  191 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.6261 (mttt)
REVERT: A  256 TYR cc_start: 0.6374 (t80) cc_final: 0.5815 (t80)
REVERT: A  273 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5829 (mm)
REVERT: A  287 GLU cc_start: 0.7966 (pp20) cc_final: 0.7575 (pp20)
REVERT: B   87 LYS cc_start: 0.7926 (mmmm) cc_final: 0.7239 (pttm)
REVERT: B  184 GLN cc_start: 0.7614 (mm-40) cc_final: 0.6453 (pt0)
REVERT: B  338 MET cc_start: 0.6923 (tpp) cc_final: 0.6520 (mmm)
  outliers start: 19
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0891
  time to fit residues: 12.5921
Evaluate side-chains
  123 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.4558

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.112992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.103864 restraints weight = 16486.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.105723 restraints weight = 9634.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.106951 restraints weight = 6198.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.107787 restraints weight = 4297.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.108416 restraints weight = 3163.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4878  Z= 0.144
  Angle     :  0.632   7.319   6727  Z= 0.351
  Chirality :  0.042   0.149    770
  Planarity :  0.005   0.055    720
  Dihedral  : 22.117  79.088    933
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 20.34 %
    Favored  : 74.82 %
  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: -2.21 (0.39), residues: 482
  helix:  0.05 (0.44), residues: 146
  sheet: -1.96 (0.50), residues: 99
  loop : -2.23 (0.42), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 250 
 TYR   0.007   0.001   TYR B 195 
 PHE   0.011   0.001   PHE B 171 
 TRP   0.004   0.001   TRP B 420 
 HIS   0.005   0.001   HIS A 136 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.14 ( 4878)
  covalent geometry    : angle       0.63168 /  0.35 ( 6727)
  hydrogen bonds       : bond        0.05608 /  3.89 (  173)
  hydrogen bonds       : angle       5.15148 /  3.72 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7150 (pp)
REVERT: A  191 LYS cc_start: 0.6644 (OUTLIER) cc_final: 0.6266 (mttt)
REVERT: A  256 TYR cc_start: 0.6348 (t80) cc_final: 0.5819 (t80)
REVERT: A  273 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5826 (mm)
REVERT: A  287 GLU cc_start: 0.7963 (pp20) cc_final: 0.7595 (pp20)
REVERT: B   83 ARG cc_start: 0.7332 (mtm110) cc_final: 0.7129 (mtm110)
REVERT: B   87 LYS cc_start: 0.7893 (mmmm) cc_final: 0.7179 (ptpp)
REVERT: B  184 GLN cc_start: 0.7596 (mm-40) cc_final: 0.6491 (pt0)
REVERT: B  338 MET cc_start: 0.6888 (tpp) cc_final: 0.6481 (mmm)
  outliers start: 20
  outliers final: 12
  residues processed: 117
  average time/residue: 0.0727
  time to fit residues: 10.3438
Evaluate side-chains
  119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 40 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.5138

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.112207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.103130 restraints weight = 16938.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.104974 restraints weight = 10081.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.106222 restraints weight = 6585.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.107097 restraints weight = 4597.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.107743 restraints weight = 3380.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4878  Z= 0.147
  Angle     :  0.629   7.906   6727  Z= 0.350
  Chirality :  0.041   0.138    770
  Planarity :  0.004   0.037    720
  Dihedral  : 22.069  76.042    933
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 23.49 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.39), residues: 482
  helix:  0.07 (0.44), residues: 146
  sheet: -1.90 (0.51), residues: 99
  loop : -2.22 (0.41), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.012   0.001   TYR B 340 
 PHE   0.018   0.002   PHE A 110 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.005   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.15 ( 4878)
  covalent geometry    : angle       0.62869 /  0.35 ( 6727)
  hydrogen bonds       : bond        0.05454 /  3.79 (  173)
  hydrogen bonds       : angle       5.03234 /  3.66 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6996 (pp)
REVERT: A  191 LYS cc_start: 0.6655 (OUTLIER) cc_final: 0.6280 (mttt)
REVERT: A  273 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5824 (mm)
REVERT: A  287 GLU cc_start: 0.7967 (pp20) cc_final: 0.7644 (pp20)
REVERT: B   87 LYS cc_start: 0.7859 (mmmm) cc_final: 0.7215 (pttm)
REVERT: B  184 GLN cc_start: 0.7564 (mm-40) cc_final: 0.6554 (pt0)
REVERT: B  338 MET cc_start: 0.6888 (tpp) cc_final: 0.6472 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 113
  average time/residue: 0.0890
  time to fit residues: 12.1335
Evaluate side-chains
  119 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 40 optimal weight:    0.4980
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.111307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.102321 restraints weight = 17434.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.104172 restraints weight = 10290.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.105416 restraints weight = 6698.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.106276 restraints weight = 4657.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.106920 restraints weight = 3416.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4878  Z= 0.168
  Angle     :  0.649   7.640   6727  Z= 0.361
  Chirality :  0.042   0.138    770
  Planarity :  0.004   0.037    720
  Dihedral  : 22.034  70.832    933
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.88 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.97 %
    Favored  : 70.70 %
  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: -2.28 (0.38), residues: 482
  helix: -0.01 (0.43), residues: 146
  sheet: -1.92 (0.51), residues: 99
  loop : -2.32 (0.40), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.009   0.001   TYR A 307 
 PHE   0.013   0.002   PHE A 244 
 TRP   0.008   0.002   TRP A 318 
 HIS   0.006   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.17 ( 4878)
  covalent geometry    : angle       0.64885 /  0.36 ( 6727)
  hydrogen bonds       : bond        0.05670 /  3.94 (  173)
  hydrogen bonds       : angle       5.00955 /  3.64 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6858 (pp)
REVERT: A  191 LYS cc_start: 0.6683 (OUTLIER) cc_final: 0.6295 (mttt)
REVERT: A  273 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5772 (mm)
REVERT: A  287 GLU cc_start: 0.7999 (pp20) cc_final: 0.7698 (pp20)
REVERT: B   87 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7210 (pttm)
REVERT: B  184 GLN cc_start: 0.7812 (mm-40) cc_final: 0.6688 (pt0)
REVERT: B  250 ARG cc_start: 0.3776 (ttt180) cc_final: 0.3525 (ttp-170)
REVERT: B  338 MET cc_start: 0.6912 (tpp) cc_final: 0.6479 (mmm)
  outliers start: 22
  outliers final: 18
  residues processed: 117
  average time/residue: 0.0755
  time to fit residues: 10.8013
Evaluate side-chains
  121 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 100
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  199 VAL
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0060
   chunk 43 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0980
   chunk 9 optimal weight:    0.2980
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 46 optimal weight:    0.4980
   overall best weight:    0.2996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.112670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.103312 restraints weight = 16715.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.105243 restraints weight = 9702.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.106550 restraints weight = 6236.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.107434 restraints weight = 4299.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.107972 restraints weight = 3146.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4878  Z= 0.132
  Angle     :  0.632   8.029   6727  Z= 0.350
  Chirality :  0.041   0.128    770
  Planarity :  0.004   0.039    720
  Dihedral  : 22.005  65.998    933
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 23.73 %
    Favored  : 70.70 %
  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: -2.07 (0.39), residues: 482
  helix:  0.13 (0.44), residues: 147
  sheet: -1.74 (0.52), residues: 99
  loop : -2.21 (0.41), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  83 
 TYR   0.008   0.001   TYR B 340 
 PHE   0.015   0.001   PHE A 244 
 TRP   0.004   0.001   TRP B 420 
 HIS   0.004   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.13 ( 4878)
  covalent geometry    : angle       0.63241 /  0.35 ( 6727)
  hydrogen bonds       : bond        0.05024 /  3.48 (  173)
  hydrogen bonds       : angle       4.80933 /  3.53 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6867 (pp)
REVERT: A  191 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6260 (mttt)
REVERT: A  287 GLU cc_start: 0.8023 (pp20) cc_final: 0.7780 (pp20)
REVERT: B   83 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7109 (mtm110)
REVERT: B   85 ARG cc_start: 0.6985 (mtt-85) cc_final: 0.6671 (mtp180)
REVERT: B   87 LYS cc_start: 0.7791 (mmmm) cc_final: 0.7175 (pttm)
REVERT: B  184 GLN cc_start: 0.7772 (mm-40) cc_final: 0.6647 (pt0)
REVERT: B  250 ARG cc_start: 0.3852 (ttt180) cc_final: 0.3624 (ttp-170)
REVERT: B  338 MET cc_start: 0.6887 (tpp) cc_final: 0.6470 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0998
  time to fit residues: 13.7520
Evaluate side-chains
  122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0470
   chunk 45 optimal weight:    0.0370
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4156

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.112337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.102858 restraints weight = 17009.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.104815 restraints weight = 9902.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.106134 restraints weight = 6367.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.107019 restraints weight = 4396.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.107635 restraints weight = 3229.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.2259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4878  Z= 0.141
  Angle     :  0.635   8.100   6727  Z= 0.351
  Chirality :  0.041   0.155    770
  Planarity :  0.004   0.036    720
  Dihedral  : 21.958  65.407    933
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.97 %
    Favored  : 70.70 %
  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: -2.10 (0.39), residues: 482
  helix: -0.09 (0.43), residues: 153
  sheet: -1.69 (0.52), residues: 99
  loop : -2.16 (0.41), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.008   0.001   TYR B 195 
 PHE   0.012   0.001   PHE A 244 
 TRP   0.004   0.001   TRP A 318 
 HIS   0.005   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.14 ( 4878)
  covalent geometry    : angle       0.63545 /  0.35 ( 6727)
  hydrogen bonds       : bond        0.05012 /  3.44 (  173)
  hydrogen bonds       : angle       4.79347 /  3.52 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6831 (pp)
REVERT: A  191 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6297 (mttt)
REVERT: A  287 GLU cc_start: 0.7997 (pp20) cc_final: 0.7742 (pp20)
REVERT: B   83 ARG cc_start: 0.7411 (mtm110) cc_final: 0.6975 (mtm110)
REVERT: B   87 LYS cc_start: 0.7802 (mmmm) cc_final: 0.7189 (pttm)
REVERT: B  184 GLN cc_start: 0.7780 (mm-40) cc_final: 0.6644 (pt0)
REVERT: B  338 MET cc_start: 0.6893 (tpp) cc_final: 0.6473 (mmm)
  outliers start: 22
  outliers final: 20
  residues processed: 110
  average time/residue: 0.0997
  time to fit residues: 13.0872
Evaluate side-chains
  122 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   29 LYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  122 THR
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Chi-restraints excluded: chain B residue  434 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 45 optimal weight:    0.1980
   chunk 10 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 21 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0470
   chunk 20 optimal weight:    0.9990
   chunk 47 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0040
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.1890

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.113323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.104008 restraints weight = 16821.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.105912 restraints weight = 9935.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.107197 restraints weight = 6452.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.108081 restraints weight = 4493.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.108751 restraints weight = 3310.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6502
moved from start:          0.2427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4878  Z= 0.123
  Angle     :  0.627   8.820   6727  Z= 0.343
  Chirality :  0.040   0.142    770
  Planarity :  0.004   0.038    720
  Dihedral  : 21.924  63.843    933
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 23.73 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.39), residues: 482
  helix: -0.03 (0.43), residues: 153
  sheet: -1.70 (0.50), residues: 102
  loop : -1.99 (0.43), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 250 
 TYR   0.009   0.001   TYR B 340 
 PHE   0.012   0.001   PHE A 244 
 TRP   0.005   0.001   TRP B 420 
 HIS   0.004   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.12 ( 4878)
  covalent geometry    : angle       0.62667 /  0.34 ( 6727)
  hydrogen bonds       : bond        0.04442 /  3.04 (  173)
  hydrogen bonds       : angle       4.62492 /  3.42 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7077 (OUTLIER) cc_final: 0.6240 (pp)
REVERT: A  191 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6312 (mttt)
REVERT: A  287 GLU cc_start: 0.7925 (pp20) cc_final: 0.7664 (pp20)
REVERT: B   87 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7223 (pttm)
REVERT: B  184 GLN cc_start: 0.7718 (mm-40) cc_final: 0.6618 (pt0)
REVERT: B  338 MET cc_start: 0.6814 (tpp) cc_final: 0.6410 (mmm)
  outliers start: 20
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0935
  time to fit residues: 12.7221
Evaluate side-chains
  116 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0770
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.112410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.103433 restraints weight = 16833.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.105195 restraints weight = 10128.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.106425 restraints weight = 6680.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.107273 restraints weight = 4689.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.107897 restraints weight = 3480.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6529
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4878  Z= 0.142
  Angle     :  0.630   7.840   6727  Z= 0.345
  Chirality :  0.040   0.126    770
  Planarity :  0.004   0.036    720
  Dihedral  : 21.858  63.470    929
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 23.24 %
    Favored  : 71.67 %
  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: -1.90 (0.39), residues: 482
  helix:  0.04 (0.43), residues: 153
  sheet: -1.52 (0.53), residues: 99
  loop : -2.04 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.007   0.001   TYR B 195 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.005   0.001   TRP A 318 
 HIS   0.005   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.14 ( 4878)
  covalent geometry    : angle       0.63019 /  0.35 ( 6727)
  hydrogen bonds       : bond        0.04705 /  3.22 (  173)
  hydrogen bonds       : angle       4.59661 /  3.38 (  449)

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

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

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  964 Ramachandran restraints generated.
    482 Oldfield, 0 Emsley, 482 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6243 (pp)
REVERT: A  191 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6369 (mttt)
REVERT: A  287 GLU cc_start: 0.7925 (pp20) cc_final: 0.7659 (pp20)
REVERT: B   87 LYS cc_start: 0.7868 (mmmm) cc_final: 0.7267 (pttm)
REVERT: B  153 ARG cc_start: 0.5779 (OUTLIER) cc_final: 0.4246 (tpp80)
REVERT: B  184 GLN cc_start: 0.7750 (mm-40) cc_final: 0.6647 (pt0)
REVERT: B  338 MET cc_start: 0.6862 (tpp) cc_final: 0.6456 (mmm)
  outliers start: 21
  outliers final: 18
  residues processed: 110
  average time/residue: 0.0929
  time to fit residues: 12.4859
Evaluate side-chains
  120 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 LEU
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   34 PHE
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   95 LEU
Chi-restraints excluded: chain A residue  138 CYS
Chi-restraints excluded: chain A residue  140 HIS
Chi-restraints excluded: chain A residue  172 MET
Chi-restraints excluded: chain A residue  191 LYS
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  223 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain B residue   99 VAL
Chi-restraints excluded: chain B residue  153 ARG
Chi-restraints excluded: chain B residue  195 TYR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 ARG
Chi-restraints excluded: chain B residue  361 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 48 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 35 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    0.1980
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.4380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 322 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.112565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.103335 restraints weight = 17125.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.105196 restraints weight = 10181.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.106445 restraints weight = 6644.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.107308 restraints weight = 4657.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.107971 restraints weight = 3452.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6528
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4878  Z= 0.137
  Angle     :  0.632   8.488   6727  Z= 0.344
  Chirality :  0.040   0.149    770
  Planarity :  0.004   0.036    720
  Dihedral  : 21.827  63.256    929
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 23.00 %
    Favored  : 71.67 %
  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: -1.90 (0.39), residues: 482
  helix:  0.06 (0.43), residues: 153
  sheet: -1.51 (0.52), residues: 101
  loop : -2.06 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.008   0.001   TYR B 195 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.006   0.001   TRP A 318 
 HIS   0.004   0.001   HIS B 384 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.14 ( 4878)
  covalent geometry    : angle       0.63185 /  0.34 ( 6727)
  hydrogen bonds       : bond        0.04654 /  3.18 (  173)
  hydrogen bonds       : angle       4.55937 /  3.36 (  449)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1057.36 seconds
wall clock time: 18 minutes 51.79 seconds (1131.79 seconds total)