Starting phenix.real_space_refine
on Wed Apr 30 19:15:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5fn4_3239/04_2025/5fn4_3239.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    6398      2.51       5
     N    1596      2.21       5
     O    1747      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9776
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5222
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5222
          Classifications: {'peptide': 665}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627}
    Chain: "B"
      Number of atoms: 1714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1714
          Classifications: {'peptide': 217}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 210}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 1868
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1868
          Classifications: {'peptide': 243}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 235}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "D"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 847
          Classifications: {'peptide': 100}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "G"
      Number of atoms: 125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 125
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
  Time building chain proxies: 5.95, per 1000 atoms: 0.61
  Number of scatterers: 9776
  At special positions: 0
  Unit cell: (91, 142.8, 103.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      35     16.00
     O    1747      8.00
     N    1596      7.00
     C    6398      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  50 " - pdb=" SG  CYS A  62 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 140 " - pdb=" SG  CYS A 159 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 213 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 230 " - pdb=" SG  CYS A 248 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 620 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2352

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 6 sheets defined
      60.1% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 40
    Processing helix  chain 'A' and resid 78 through 87
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 185 through 200
      removed outlier: 4.354A  pdb=" N   THR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.862A  pdb=" N   CYS A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 315
    Processing helix  chain 'A' and resid 339 through 350
    Processing helix  chain 'A' and resid 381 through 387
      removed outlier: 3.640A  pdb=" N   ASN A 387 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 407
      removed outlier: 3.829A  pdb=" N   GLY A 407 " --> pdb=" O   LYS A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 431
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 474 through 478
    Processing helix  chain 'A' and resid 481 through 502
    Processing helix  chain 'A' and resid 514 through 527
      removed outlier: 3.651A  pdb=" N   VAL A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 538
    Processing helix  chain 'A' and resid 561 through 576
      removed outlier: 3.530A  pdb=" N   VAL A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 588
    Processing helix  chain 'A' and resid 596 through 600
      removed outlier: 3.775A  pdb=" N   TYR A 600 " --> pdb=" O   LYS A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 637
    Processing helix  chain 'A' and resid 665 through 693
    Processing helix  chain 'A' and resid 693 through 698
      removed outlier: 3.901A  pdb=" N   LEU A 697 " --> pdb=" O   LYS A 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 104
      Proline residue:  B  88  - end of helix
      removed outlier: 4.039A  pdb=" N   SER B 104 " --> pdb=" O   ILE B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 190
      removed outlier: 3.533A  pdb=" N   PHE B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 214
    Processing helix  chain 'B' and resid 219 through 241
    Processing helix  chain 'B' and resid 242 through 262
    Processing helix  chain 'B' and resid 382 through 399
    Processing helix  chain 'B' and resid 403 through 428
      removed outlier: 3.503A  pdb=" N   THR B 407 " --> pdb=" O   ASP B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 452
    Processing helix  chain 'B' and resid 452 through 464
      removed outlier: 4.420A  pdb=" N   PHE B 456 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 25
      Proline residue:  C  16  - end of helix
    Processing helix  chain 'C' and resid 28 through 61
      removed outlier: 3.626A  pdb=" N   THR C  60 " --> pdb=" O   LEU C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 64 through 100
      removed outlier: 4.077A  pdb=" N   GLY C 100 " --> pdb=" O   LYS C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 142
      removed outlier: 3.864A  pdb=" N   MET C 117 " --> pdb=" O   SER C 113 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   ASN C 136 " --> pdb=" O   PHE C 132 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   ILE C 137 " --> pdb=" O   SER C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 185
      removed outlier: 3.874A  pdb=" N   THR C 159 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR C 172 " --> pdb=" O   ILE C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 206
      removed outlier: 4.295A  pdb=" N   LEU C 190 " --> pdb=" O   ARG C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 212
    Processing helix  chain 'C' and resid 213 through 232
    Processing helix  chain 'C' and resid 235 through 243
      removed outlier: 3.704A  pdb=" N   ILE C 239 " --> pdb=" O   SER C 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 6
      removed outlier: 4.207A  pdb=" N   ARG D   5 " --> pdb=" O   ASN D   2 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 7 through 23
    Processing helix  chain 'D' and resid 26 through 43
      removed outlier: 4.312A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 49 through 85
      Proline residue:  D  83  - end of helix
    Processing helix  chain 'D' and resid 86 through 92
    Processing helix  chain 'G' and resid -1 through 23
    Processing sheet with id=AA, first strand: chain 'A' and resid 41 through 44
      removed outlier: 4.673A  pdb=" N   ALA A 658 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
    Processing sheet with id=AB, first strand: chain 'A' and resid 59 through 60
    Processing sheet with id=AC, first strand: chain 'A' and resid 72 through 76
      removed outlier: 4.425A  pdb=" N   GLU A  99 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing sheet with id=AD, first strand: chain 'A' and resid 377 through 379
      removed outlier: 3.635A  pdb=" N   SER A 361 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing sheet with id=AE, first strand: chain 'A' and resid 577 through 579
      removed outlier: 4.172A  pdb=" N   CYS A 620 " --> pdb=" O   VAL A 579 " (cutoff:3.500A)
    Processing sheet with id=BA, first strand: chain 'B' and resid 193 through 194
      removed outlier: 6.858A  pdb=" N   VAL B 193 " --> pdb=" O   PHE D  94 " (cutoff:3.500A)

    594 hydrogen bonds defined for protein.
    1737 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.88

  Time building geometry restraints manager: 3.22 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1685
        1.32 -     1.45: 2759
        1.45 -     1.57: 5523
        1.57 -     1.70: 8
        1.70 -     1.82: 53
  Bond restraints: 10028
  Sorted by residual:
  bond pdb=" C   LEU C 244 "
       pdb=" O   LEU C 244 "
    ideal  model  delta    sigma   weight residual
    1.231  1.380 -0.149 2.00e-02 2.50e+03 5.53e+01
  bond pdb=" C   HIS C 197 "
       pdb=" O   HIS C 197 "
    ideal  model  delta    sigma   weight residual
    1.236  1.304 -0.067 1.15e-02 7.56e+03 3.42e+01
  bond pdb=" CA  VAL B  87 "
       pdb=" CB  VAL B  87 "
    ideal  model  delta    sigma   weight residual
    1.539  1.562 -0.023 5.40e-03 3.43e+04 1.77e+01
  bond pdb=" CA  VAL B 255 "
       pdb=" CB  VAL B 255 "
    ideal  model  delta    sigma   weight residual
    1.540  1.582 -0.042 1.17e-02 7.31e+03 1.31e+01
  bond pdb=" N   PHE B  86 "
       pdb=" CA  PHE B  86 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.042 1.17e-02 7.31e+03 1.28e+01
  ... (remaining 10023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 11458
        2.48 -     4.96: 2064
        4.96 -     7.44: 121
        7.44 -     9.92: 26
        9.92 -    12.40: 6
  Bond angle restraints: 13675
  Sorted by residual:
  angle pdb=" O   ALA G  22 "
        pdb=" C   ALA G  22 "
        pdb=" N   ALA G  23 "
      ideal   model   delta    sigma   weight residual
     122.07  109.70   12.37 1.03e+00 9.43e-01 1.44e+02
  angle pdb=" O   ALA G  21 "
        pdb=" C   ALA G  21 "
        pdb=" N   ALA G  22 "
      ideal   model   delta    sigma   weight residual
     122.07  109.73   12.34 1.03e+00 9.43e-01 1.44e+02
  angle pdb=" N   ILE A 162 "
        pdb=" CA  ILE A 162 "
        pdb=" C   ILE A 162 "
      ideal   model   delta    sigma   weight residual
     111.62  118.93   -7.31 7.90e-01 1.60e+00 8.55e+01
  angle pdb=" O   VAL B  87 "
        pdb=" C   VAL B  87 "
        pdb=" N   PRO B  88 "
      ideal   model   delta    sigma   weight residual
     120.42  125.11   -4.69 6.40e-01 2.44e+00 5.38e+01
  angle pdb=" CA  LEU C 169 "
        pdb=" C   LEU C 169 "
        pdb=" N   LEU C 170 "
      ideal   model   delta    sigma   weight residual
     117.07  108.87    8.20 1.14e+00 7.69e-01 5.18e+01
  ... (remaining 13670 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4964
       17.74 -    35.47: 643
       35.47 -    53.21: 188
       53.21 -    70.95: 44
       70.95 -    88.68: 12
  Dihedral angle restraints: 5851
    sinusoidal: 2208
      harmonic: 3643
  Sorted by residual:
  dihedral pdb=" CB  CYS A 586 "
           pdb=" SG  CYS A 586 "
           pdb=" SG  CYS A 620 "
           pdb=" CB  CYS A 620 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.38   82.38     1      1.00e+01 1.00e-02 8.33e+01
  dihedral pdb=" CB  CYS A 140 "
           pdb=" SG  CYS A 140 "
           pdb=" SG  CYS A 159 "
           pdb=" CB  CYS A 159 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.51  -75.51     1      1.00e+01 1.00e-02 7.20e+01
  dihedral pdb=" CB  CYS A 230 "
           pdb=" SG  CYS A 230 "
           pdb=" SG  CYS A 248 "
           pdb=" CB  CYS A 248 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.50  -69.50     1      1.00e+01 1.00e-02 6.24e+01
  ... (remaining 5848 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1310
       0.120 -    0.240: 235
       0.240 -    0.360: 30
       0.360 -    0.480: 8
       0.480 -    0.600: 1
  Chirality restraints: 1584
  Sorted by residual:
  chirality pdb=" CA  PHE A 302 "
            pdb=" N   PHE A 302 "
            pdb=" C   PHE A 302 "
            pdb=" CB  PHE A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 9.00e+00
  chirality pdb=" CA  PHE A 218 "
            pdb=" N   PHE A 218 "
            pdb=" C   PHE A 218 "
            pdb=" CB  PHE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.90e+00
  chirality pdb=" CA  LEU A 312 "
            pdb=" N   LEU A 312 "
            pdb=" C   LEU A 312 "
            pdb=" CB  LEU A 312 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.07    0.44 2.00e-01 2.50e+01 4.75e+00
  ... (remaining 1581 not shown)

  Planarity restraints: 1706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  21 "   -0.067 2.00e-02 2.50e+03   1.25e-01 1.56e+02
        pdb=" C   ALA G  21 "    0.216 2.00e-02 2.50e+03
        pdb=" O   ALA G  21 "   -0.080 2.00e-02 2.50e+03
        pdb=" N   ALA G  22 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA G  22 "   -0.067 2.00e-02 2.50e+03   1.25e-01 1.55e+02
        pdb=" C   ALA G  22 "    0.216 2.00e-02 2.50e+03
        pdb=" O   ALA G  22 "   -0.080 2.00e-02 2.50e+03
        pdb=" N   ALA G  23 "   -0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 175 "    0.020 2.00e-02 2.50e+03   4.22e-02 1.78e+01
        pdb=" C   PHE B 175 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   PHE B 175 "    0.028 2.00e-02 2.50e+03
        pdb=" N   PHE B 176 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1703 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 180
        2.69 -     3.24: 10256
        3.24 -     3.79: 16234
        3.79 -     4.35: 20802
        4.35 -     4.90: 32959
  Nonbonded interactions: 80431
  Sorted by model distance:
  nonbonded pdb=" O   LEU C  35 "
            pdb=" OG  SER C 124 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" O   HIS C 197 "
            pdb=" OG1 THR C 200 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   PHE B 445 "
            pdb=" OG1 THR B 449 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ALA C  76 "
            pdb=" OG  SER C  79 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   ARG A 232 "
            pdb=" OG  SER A 235 "
     model   vdw
     2.294 3.040
  ... (remaining 80426 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.300
  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:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.580
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5710
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      :  0.010   0.149  10033  Z= 0.663
  Angle     :  1.714  12.399  13685  Z= 1.235
  Chirality :  0.096   0.600   1584
  Planarity :  0.009   0.125   1706
  Dihedral  : 18.066  88.682   3484
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  3.24 %
    Allowed  : 11.98 %
    Favored  : 84.78 %
  Rotamer:
    Outliers : 10.51 %
    Allowed  : 14.90 %
    Favored  : 74.59 %
  Cbeta Deviations :  1.45 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.21), residues: 1235
  helix:  1.03 (0.16), residues: 712
  sheet: -3.69 (0.40), residues: 110
  loop : -3.87 (0.25), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP D  36 
 HIS   0.017   0.003   HIS A 553 
 PHE   0.044   0.004   PHE B 176 
 TYR   0.043   0.004   TYR C  69 
 ARG   0.006   0.001   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14051 (  594)
  hydrogen bonds       : angle       5.73107 ( 1737)
  SS BOND              : bond        0.01344 (    5)
  SS BOND              : angle       2.28809 (   10)
  covalent geometry    : bond        0.00980 (10028)
  covalent geometry    : angle       1.71310 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 316
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 ILE cc_start: 0.9434 (mt) cc_final: 0.9226 (mt)
REVERT: A   95 MET cc_start: 0.8348 (mmt) cc_final: 0.7925 (mmm)
REVERT: A  100 SER cc_start: 0.9257 (OUTLIER) cc_final: 0.8679 (p)
REVERT: A  215 MET cc_start: 0.8953 (ttp) cc_final: 0.8743 (ptm)
REVERT: A  217 LEU cc_start: 0.8876 (tt) cc_final: 0.8541 (pt)
REVERT: A  231 MET cc_start: 0.8855 (mmp) cc_final: 0.8583 (mmm)
REVERT: A  249 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7623 (m-30)
REVERT: A  259 MET cc_start: 0.9163 (tpp) cc_final: 0.8757 (mmm)
REVERT: A  331 GLN cc_start: 0.7945 (tp-100) cc_final: 0.7703 (tp40)
REVERT: A  347 MET cc_start: 0.9318 (mtm) cc_final: 0.9057 (mpp)
REVERT: A  362 PHE cc_start: 0.8225 (t80) cc_final: 0.7950 (t80)
REVERT: A  474 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8837 (pp20)
REVERT: A  543 ARG cc_start: 0.8527 (ptm-80) cc_final: 0.7886 (tpt170)
REVERT: A  548 ASP cc_start: 0.9101 (t0) cc_final: 0.8835 (m-30)
REVERT: A  574 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8476 (mt)
REVERT: A  575 THR cc_start: 0.7571 (p) cc_final: 0.7207 (p)
REVERT: A  649 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.6472 (t)
REVERT: B   93 MET cc_start: 0.9294 (mtm) cc_final: 0.9071 (mmt)
REVERT: B  106 TYR cc_start: 0.8629 (m-80) cc_final: 0.8246 (m-80)
REVERT: B  167 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6393 (tp)
REVERT: B  184 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8585 (mm-30)
REVERT: B  223 GLN cc_start: 0.8384 (mt0) cc_final: 0.7849 (mm-40)
REVERT: B  244 TRP cc_start: 0.5553 (OUTLIER) cc_final: 0.4638 (m100)
REVERT: B  389 TYR cc_start: 0.8875 (m-80) cc_final: 0.8174 (m-80)
REVERT: B  399 THR cc_start: 0.7568 (m) cc_final: 0.7333 (t)
REVERT: B  419 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9010 (m)
REVERT: B  456 PHE cc_start: 0.9405 (t80) cc_final: 0.9175 (t80)
REVERT: C   24 THR cc_start: 0.9022 (m) cc_final: 0.8773 (p)
REVERT: C   53 TRP cc_start: 0.8627 (t60) cc_final: 0.7886 (t60)
REVERT: C   91 TYR cc_start: 0.8963 (t80) cc_final: 0.8735 (t80)
REVERT: C   99 GLU cc_start: 0.8916 (pt0) cc_final: 0.8684 (pt0)
REVERT: D   84 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8485 (mpt-90)
REVERT: D   95 THR cc_start: 0.8328 (m) cc_final: 0.8011 (p)
  outliers start: 110
  outliers final: 34
  residues processed: 384
  average time/residue: 0.2077
  time to fit residues: 112.1946
Evaluate side-chains
  262 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 219
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 GLN
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  474 GLU
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  574 LEU
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  244 TRP
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  419 CYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  423 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  193 VAL
Chi-restraints excluded: chain D residue   47 TYR
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   85 TRP
Chi-restraints excluded: chain D residue   93 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    0.9990
   chunk 37 optimal weight:   30.0000
   chunk 58 optimal weight:    5.9990
   chunk 71 optimal weight:    0.3980
   chunk 111 optimal weight:    0.9990
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
A 305 GLN
A 355 GLN
A 417 ASN
A 428 GLN
A 450 ASN
A 478 ASN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 612 ASN
B 223 GLN
** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.068907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.057827 restraints weight = 48284.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.059551 restraints weight = 27510.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.060686 restraints weight = 18126.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10033  Z= 0.168
  Angle     :  0.841  10.853  13685  Z= 0.423
  Chirality :  0.046   0.209   1584
  Planarity :  0.006   0.061   1706
  Dihedral  :  9.999  66.372   1420
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  1.38 %
    Allowed  :  7.77 %
    Favored  : 90.85 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 20.15 %
    Favored  : 73.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.25), residues: 1235
  helix:  2.60 (0.19), residues: 716
  sheet: -3.18 (0.37), residues: 119
  loop : -3.39 (0.27), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  36 
 HIS   0.012   0.002   HIS A 553 
 PHE   0.031   0.002   PHE A 302 
 TYR   0.021   0.002   TYR A 565 
 ARG   0.004   0.001   ARG C 237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04545 (  594)
  hydrogen bonds       : angle       4.50612 ( 1737)
  SS BOND              : bond        0.00480 (    5)
  SS BOND              : angle       2.38028 (   10)
  covalent geometry    : bond        0.00355 (10028)
  covalent geometry    : angle       0.83892 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 263
  time to evaluate  : 1.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 TYR cc_start: 0.2645 (t80) cc_final: 0.1985 (t80)
REVERT: A  186 GLU cc_start: 0.9089 (tt0) cc_final: 0.8730 (tp30)
REVERT: A  249 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8000 (m-30)
REVERT: A  325 VAL cc_start: 0.9605 (t) cc_final: 0.9312 (t)
REVERT: A  343 MET cc_start: 0.8823 (tpp) cc_final: 0.8512 (tpt)
REVERT: A  362 PHE cc_start: 0.8730 (t80) cc_final: 0.7564 (t80)
REVERT: A  378 MET cc_start: 0.8160 (mpt) cc_final: 0.7439 (mpp)
REVERT: A  413 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8829 (tt)
REVERT: A  428 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.7842 (pt0)
REVERT: A  526 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9016 (tp)
REVERT: A  546 LEU cc_start: 0.9451 (mt) cc_final: 0.9209 (mt)
REVERT: A  548 ASP cc_start: 0.8981 (t0) cc_final: 0.8687 (m-30)
REVERT: B  168 ILE cc_start: 0.7495 (mm) cc_final: 0.7216 (mm)
REVERT: B  184 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8957 (mm-30)
REVERT: B  203 TRP cc_start: 0.9208 (t-100) cc_final: 0.8866 (t-100)
REVERT: B  223 GLN cc_start: 0.8527 (mt0) cc_final: 0.7846 (mm-40)
REVERT: B  244 TRP cc_start: 0.5019 (OUTLIER) cc_final: 0.4734 (m100)
REVERT: B  412 VAL cc_start: 0.9633 (t) cc_final: 0.9420 (p)
REVERT: B  441 PHE cc_start: 0.8757 (m-80) cc_final: 0.8443 (m-80)
REVERT: B  458 ASP cc_start: 0.9079 (t0) cc_final: 0.8821 (m-30)
REVERT: C   43 LEU cc_start: 0.9364 (mt) cc_final: 0.8972 (mt)
REVERT: C   69 TYR cc_start: 0.8670 (t80) cc_final: 0.8450 (t80)
REVERT: C   83 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8663 (mm-40)
REVERT: C   93 LEU cc_start: 0.9255 (mt) cc_final: 0.8975 (tt)
REVERT: C  127 ILE cc_start: 0.9475 (OUTLIER) cc_final: 0.9249 (mp)
REVERT: D   20 LEU cc_start: 0.8388 (mt) cc_final: 0.8134 (pp)
REVERT: D   38 PHE cc_start: 0.8555 (t80) cc_final: 0.8302 (t80)
REVERT: D   62 VAL cc_start: 0.8688 (t) cc_final: 0.8453 (m)
REVERT: D   76 THR cc_start: 0.8954 (m) cc_final: 0.8712 (p)
  outliers start: 66
  outliers final: 30
  residues processed: 307
  average time/residue: 0.2183
  time to fit residues: 98.4104
Evaluate side-chains
  230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  140 CYS
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  428 GLN
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  644 GLU
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  184 GLU
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  244 TRP
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain D residue   68 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 72 optimal weight:   10.0000
   chunk 23 optimal weight:    0.0970
   chunk 47 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    5.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 222 HIS
A 305 GLN
A 313 GLN
** A 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 367 GLN
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 ASN
A 535 GLN
A 606 GLN
B 190 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.064937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.054091 restraints weight = 51236.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.055568 restraints weight = 29061.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.056788 restraints weight = 19368.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098  10033  Z= 0.293
  Angle     :  0.872  20.529  13685  Z= 0.443
  Chirality :  0.047   0.309   1584
  Planarity :  0.006   0.067   1706
  Dihedral  :  8.382  62.896   1379
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.97 %
    Allowed  :  8.50 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  7.74 %
    Allowed  : 21.39 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.25), residues: 1235
  helix:  1.88 (0.19), residues: 711
  sheet: -3.15 (0.37), residues: 124
  loop : -3.17 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP C 174 
 HIS   0.008   0.002   HIS A 553 
 PHE   0.040   0.003   PHE B 465 
 TYR   0.025   0.002   TYR B 225 
 ARG   0.005   0.001   ARG A 543 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04549 (  594)
  hydrogen bonds       : angle       4.77136 ( 1737)
  SS BOND              : bond        0.01427 (    5)
  SS BOND              : angle       3.82442 (   10)
  covalent geometry    : bond        0.00640 (10028)
  covalent geometry    : angle       0.86662 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 196
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 TYR cc_start: 0.2986 (t80) cc_final: 0.1805 (t80)
REVERT: A  186 GLU cc_start: 0.8990 (tt0) cc_final: 0.8740 (tp30)
REVERT: A  221 MET cc_start: 0.8847 (mmp) cc_final: 0.8081 (tpp)
REVERT: A  253 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6751 (p0)
REVERT: A  343 MET cc_start: 0.8888 (tpp) cc_final: 0.8605 (tpt)
REVERT: A  362 PHE cc_start: 0.8874 (t80) cc_final: 0.8197 (t80)
REVERT: A  378 MET cc_start: 0.8296 (mpt) cc_final: 0.7636 (mpp)
REVERT: A  413 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8825 (tt)
REVERT: A  526 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9386 (mm)
REVERT: A  546 LEU cc_start: 0.9524 (mt) cc_final: 0.9240 (mt)
REVERT: A  548 ASP cc_start: 0.9066 (t0) cc_final: 0.8715 (m-30)
REVERT: B   84 MET cc_start: 0.8972 (ptt) cc_final: 0.8624 (ptt)
REVERT: B  203 TRP cc_start: 0.9034 (t-100) cc_final: 0.8778 (t-100)
REVERT: B  244 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.5025 (m100)
REVERT: B  399 THR cc_start: 0.8373 (m) cc_final: 0.8093 (t)
REVERT: B  441 PHE cc_start: 0.8984 (m-80) cc_final: 0.8649 (m-80)
REVERT: B  458 ASP cc_start: 0.8947 (t0) cc_final: 0.8692 (m-30)
REVERT: C   43 LEU cc_start: 0.9520 (mt) cc_final: 0.9134 (mt)
REVERT: C   83 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8440 (mm-40)
REVERT: C   93 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8971 (tt)
REVERT: C  112 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: C  135 ILE cc_start: 0.9607 (tp) cc_final: 0.9275 (pt)
REVERT: C  138 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9422 (mt)
REVERT: D   18 TYR cc_start: 0.8244 (m-80) cc_final: 0.7983 (m-80)
REVERT: D   38 PHE cc_start: 0.8657 (t80) cc_final: 0.8429 (t80)
  outliers start: 81
  outliers final: 49
  residues processed: 248
  average time/residue: 0.1904
  time to fit residues: 71.4741
Evaluate side-chains
  236 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 179
  time to evaluate  : 1.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  526 LEU
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  640 TRP
Chi-restraints excluded: chain A residue  669 GLU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  244 TRP
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  415 LEU
Chi-restraints excluded: chain B residue  416 ILE
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 100 optimal weight:    0.2980
   chunk 62 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 63 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 109 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   overall best weight:    3.8588

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 355 GLN
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
B 454 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.064992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.054341 restraints weight = 49862.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.055917 restraints weight = 28224.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.057001 restraints weight = 18517.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10033  Z= 0.228
  Angle     :  0.792  11.352  13685  Z= 0.397
  Chirality :  0.045   0.313   1584
  Planarity :  0.005   0.064   1706
  Dihedral  :  7.609  59.735   1368
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  :  7.69 %
    Favored  : 91.50 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 23.69 %
    Favored  : 69.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.25), residues: 1235
  helix:  1.76 (0.19), residues: 711
  sheet: -2.73 (0.39), residues: 124
  loop : -3.11 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 604 
 HIS   0.006   0.001   HIS A 553 
 PHE   0.038   0.002   PHE B 465 
 TYR   0.022   0.002   TYR A 554 
 ARG   0.004   0.000   ARG A 583 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04217 (  594)
  hydrogen bonds       : angle       4.65597 ( 1737)
  SS BOND              : bond        0.00536 (    5)
  SS BOND              : angle       2.45845 (   10)
  covalent geometry    : bond        0.00495 (10028)
  covalent geometry    : angle       0.78906 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 192
  time to evaluate  : 1.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 TYR cc_start: 0.3019 (t80) cc_final: 0.1622 (t80)
REVERT: A  186 GLU cc_start: 0.8978 (tt0) cc_final: 0.8742 (tp30)
REVERT: A  221 MET cc_start: 0.8932 (mmp) cc_final: 0.8208 (tpp)
REVERT: A  253 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6811 (p0)
REVERT: A  378 MET cc_start: 0.8351 (mpt) cc_final: 0.7719 (mpp)
REVERT: A  413 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.8810 (tt)
REVERT: A  546 LEU cc_start: 0.9465 (mt) cc_final: 0.9244 (mt)
REVERT: A  548 ASP cc_start: 0.8979 (t0) cc_final: 0.8657 (m-30)
REVERT: B  203 TRP cc_start: 0.9015 (t-100) cc_final: 0.8807 (t-100)
REVERT: B  399 THR cc_start: 0.8411 (m) cc_final: 0.8073 (t)
REVERT: B  441 PHE cc_start: 0.9123 (m-80) cc_final: 0.8840 (m-80)
REVERT: B  458 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8858 (m-30)
REVERT: C   43 LEU cc_start: 0.9534 (mt) cc_final: 0.9329 (mt)
REVERT: C   83 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8452 (mm-40)
REVERT: C   93 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8904 (tt)
REVERT: C  112 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8246 (tp)
REVERT: C  135 ILE cc_start: 0.9634 (tp) cc_final: 0.9239 (pt)
REVERT: C  205 PHE cc_start: 0.8537 (m-10) cc_final: 0.8334 (m-10)
REVERT: D   10 GLU cc_start: 0.9022 (tp30) cc_final: 0.8740 (tp30)
REVERT: D   76 THR cc_start: 0.9001 (m) cc_final: 0.8775 (p)
  outliers start: 71
  outliers final: 47
  residues processed: 236
  average time/residue: 0.1650
  time to fit residues: 58.9979
Evaluate side-chains
  230 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 177
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  610 HIS
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  669 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   20 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 99 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 30 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 78 optimal weight:    5.9990
   chunk 101 optimal weight:    9.9990
   chunk 106 optimal weight:    1.9990
   chunk 69 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.064405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.053707 restraints weight = 50734.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.055258 restraints weight = 28600.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056342 restraints weight = 18912.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  10033  Z= 0.260
  Angle     :  0.798  11.769  13685  Z= 0.405
  Chirality :  0.045   0.311   1584
  Planarity :  0.006   0.062   1706
  Dihedral  :  7.085  59.024   1364
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 18.03
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  8.50 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  7.26 %
    Allowed  : 24.83 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.24), residues: 1235
  helix:  1.60 (0.19), residues: 716
  sheet: -2.71 (0.39), residues: 124
  loop : -3.02 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C 174 
 HIS   0.008   0.001   HIS A 102 
 PHE   0.038   0.002   PHE B 465 
 TYR   0.023   0.002   TYR B 225 
 ARG   0.003   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  594)
  hydrogen bonds       : angle       4.76950 ( 1737)
  SS BOND              : bond        0.01158 (    5)
  SS BOND              : angle       2.82140 (   10)
  covalent geometry    : bond        0.00558 (10028)
  covalent geometry    : angle       0.79440 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 176
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 THR cc_start: 0.9526 (OUTLIER) cc_final: 0.9271 (t)
REVERT: A  186 GLU cc_start: 0.9021 (tt0) cc_final: 0.8806 (tp30)
REVERT: A  253 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7028 (p0)
REVERT: A  347 MET cc_start: 0.8627 (mpp) cc_final: 0.8167 (mpp)
REVERT: A  362 PHE cc_start: 0.8934 (t80) cc_final: 0.8568 (t80)
REVERT: A  378 MET cc_start: 0.8362 (mpt) cc_final: 0.7717 (mpp)
REVERT: A  413 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.8825 (tt)
REVERT: A  546 LEU cc_start: 0.9460 (mt) cc_final: 0.9226 (mt)
REVERT: A  548 ASP cc_start: 0.9027 (t0) cc_final: 0.8784 (m-30)
REVERT: A  689 CYS cc_start: 0.9136 (m) cc_final: 0.8786 (m)
REVERT: B  195 TYR cc_start: 0.9363 (m-80) cc_final: 0.8748 (m-80)
REVERT: B  399 THR cc_start: 0.8450 (m) cc_final: 0.8156 (t)
REVERT: B  414 ILE cc_start: 0.9586 (tp) cc_final: 0.9314 (tp)
REVERT: B  441 PHE cc_start: 0.9253 (m-80) cc_final: 0.9014 (m-80)
REVERT: B  456 PHE cc_start: 0.9143 (t80) cc_final: 0.8902 (t80)
REVERT: B  466 TYR cc_start: 0.7856 (m-10) cc_final: 0.7446 (m-10)
REVERT: C   43 LEU cc_start: 0.9592 (mt) cc_final: 0.9375 (mt)
REVERT: C   83 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8328 (mm-40)
REVERT: C   93 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9003 (tt)
REVERT: C  112 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8188 (tp)
REVERT: C  123 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9435 (tp)
REVERT: C  163 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9160 (tp)
REVERT: C  218 TYR cc_start: 0.8698 (OUTLIER) cc_final: 0.7630 (m-10)
REVERT: D   10 GLU cc_start: 0.9013 (tp30) cc_final: 0.8766 (tp30)
  outliers start: 76
  outliers final: 53
  residues processed: 225
  average time/residue: 0.1696
  time to fit residues: 59.0258
Evaluate side-chains
  234 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 172
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  640 TRP
Chi-restraints excluded: chain A residue  669 GLU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  454 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   86 PHE
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  163 LEU
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  218 TYR
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   68 VAL
Chi-restraints excluded: chain D residue   71 LEU
Chi-restraints excluded: chain D residue   75 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 110 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 237 GLN
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.066435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.056030 restraints weight = 48917.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057626 restraints weight = 27916.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.058709 restraints weight = 18431.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.5498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10033  Z= 0.149
  Angle     :  0.772  13.196  13685  Z= 0.379
  Chirality :  0.044   0.300   1584
  Planarity :  0.005   0.061   1706
  Dihedral  :  6.695  59.962   1360
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.73 %
    Allowed  :  7.45 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.18 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.25), residues: 1235
  helix:  1.74 (0.19), residues: 714
  sheet: -2.58 (0.38), residues: 124
  loop : -2.86 (0.30), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP C 174 
 HIS   0.003   0.001   HIS A 553 
 PHE   0.037   0.002   PHE B 465 
 TYR   0.018   0.001   TYR B 389 
 ARG   0.004   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03984 (  594)
  hydrogen bonds       : angle       4.51610 ( 1737)
  SS BOND              : bond        0.00340 (    5)
  SS BOND              : angle       2.68055 (   10)
  covalent geometry    : bond        0.00334 (10028)
  covalent geometry    : angle       0.76857 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 190
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  108 MET cc_start: 0.8993 (tpp) cc_final: 0.8787 (mmp)
REVERT: A  162 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6909 (pt)
REVERT: A  237 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8155 (mt0)
REVERT: A  253 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6856 (p0)
REVERT: A  259 MET cc_start: 0.8551 (mmm) cc_final: 0.8308 (tpt)
REVERT: A  343 MET cc_start: 0.8957 (tpt) cc_final: 0.8747 (tpt)
REVERT: A  347 MET cc_start: 0.8841 (mpp) cc_final: 0.8394 (mpp)
REVERT: A  689 CYS cc_start: 0.9181 (m) cc_final: 0.8856 (m)
REVERT: B  181 TYR cc_start: 0.9247 (t80) cc_final: 0.8894 (t80)
REVERT: B  195 TYR cc_start: 0.9412 (m-80) cc_final: 0.8891 (m-80)
REVERT: B  399 THR cc_start: 0.8298 (m) cc_final: 0.7930 (t)
REVERT: B  456 PHE cc_start: 0.9097 (t80) cc_final: 0.8794 (t80)
REVERT: B  459 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8281 (tp40)
REVERT: C   35 LEU cc_start: 0.9646 (tt) cc_final: 0.9368 (tp)
REVERT: C   83 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8395 (mm-40)
REVERT: C   93 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8836 (tt)
REVERT: C  112 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8212 (tp)
REVERT: C  142 LEU cc_start: 0.9105 (mt) cc_final: 0.8872 (mt)
REVERT: C  224 MET cc_start: 0.9312 (mmp) cc_final: 0.9112 (mmp)
REVERT: D   10 GLU cc_start: 0.8998 (tp30) cc_final: 0.8752 (tp30)
  outliers start: 54
  outliers final: 36
  residues processed: 219
  average time/residue: 0.1801
  time to fit residues: 60.6053
Evaluate side-chains
  207 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 165
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  454 GLN
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain D residue   66 PHE
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 59 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9980
   chunk 92 optimal weight:    6.9990
   chunk 19 optimal weight:   10.0000
   chunk 91 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 237 GLN
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.065983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.055344 restraints weight = 50157.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.056942 restraints weight = 28245.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.058130 restraints weight = 18596.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.5687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10033  Z= 0.186
  Angle     :  0.787  12.847  13685  Z= 0.390
  Chirality :  0.045   0.303   1584
  Planarity :  0.005   0.061   1706
  Dihedral  :  6.212  55.165   1356
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  8.02 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 28.75 %
    Favored  : 65.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.25), residues: 1235
  helix:  1.58 (0.19), residues: 720
  sheet: -2.37 (0.40), residues: 124
  loop : -2.87 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP C 174 
 HIS   0.011   0.001   HIS C  58 
 PHE   0.038   0.002   PHE C 132 
 TYR   0.023   0.002   TYR B 389 
 ARG   0.003   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  594)
  hydrogen bonds       : angle       4.54804 ( 1737)
  SS BOND              : bond        0.00525 (    5)
  SS BOND              : angle       1.86976 (   10)
  covalent geometry    : bond        0.00414 (10028)
  covalent geometry    : angle       0.78541 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 179
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  162 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7121 (pt)
REVERT: A  237 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8995 (pt0)
REVERT: A  253 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7013 (p0)
REVERT: A  259 MET cc_start: 0.8667 (mmm) cc_final: 0.8338 (tpt)
REVERT: A  347 MET cc_start: 0.8889 (mpp) cc_final: 0.8457 (mpp)
REVERT: A  378 MET cc_start: 0.8433 (mpp) cc_final: 0.8069 (mpp)
REVERT: A  689 CYS cc_start: 0.9193 (m) cc_final: 0.8879 (m)
REVERT: B  181 TYR cc_start: 0.9289 (t80) cc_final: 0.8919 (t80)
REVERT: B  184 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8544 (mt-10)
REVERT: B  195 TYR cc_start: 0.9401 (m-80) cc_final: 0.8874 (m-80)
REVERT: B  399 THR cc_start: 0.8310 (m) cc_final: 0.7948 (t)
REVERT: B  441 PHE cc_start: 0.9293 (m-80) cc_final: 0.8963 (m-80)
REVERT: B  450 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8487 (m-30)
REVERT: B  458 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8375 (m-30)
REVERT: B  463 HIS cc_start: 0.8881 (m90) cc_final: 0.8179 (m-70)
REVERT: C   72 LEU cc_start: 0.9029 (mt) cc_final: 0.8761 (mt)
REVERT: C   83 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8386 (mm-40)
REVERT: C   93 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8849 (tt)
REVERT: C  112 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8117 (tp)
REVERT: C  218 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8036 (m-10)
REVERT: D   10 GLU cc_start: 0.9042 (tp30) cc_final: 0.8761 (tp30)
  outliers start: 60
  outliers final: 42
  residues processed: 211
  average time/residue: 0.1647
  time to fit residues: 53.5847
Evaluate side-chains
  221 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 170
  time to evaluate  : 1.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  162 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  545 TYR
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   22 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  218 TYR
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 8 optimal weight:    9.9990
   chunk 85 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 99 optimal weight:    9.9990
   chunk 33 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 98 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0470
   chunk 115 optimal weight:    8.9990
   overall best weight:    2.4084

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 237 GLN
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 136 ASN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.066219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.055821 restraints weight = 50041.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.057374 restraints weight = 28551.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.058500 restraints weight = 18994.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10033  Z= 0.174
  Angle     :  0.791  13.599  13685  Z= 0.390
  Chirality :  0.044   0.307   1584
  Planarity :  0.005   0.061   1706
  Dihedral  :  6.042  48.862   1356
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  8.18 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 28.37 %
    Favored  : 65.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1235
  helix:  1.60 (0.19), residues: 720
  sheet: -2.30 (0.41), residues: 124
  loop : -2.80 (0.31), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP C 174 
 HIS   0.006   0.001   HIS C  58 
 PHE   0.036   0.002   PHE C 132 
 TYR   0.015   0.001   TYR A 569 
 ARG   0.003   0.000   ARG A 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  594)
  hydrogen bonds       : angle       4.59138 ( 1737)
  SS BOND              : bond        0.00980 (    5)
  SS BOND              : angle       2.62990 (   10)
  covalent geometry    : bond        0.00391 (10028)
  covalent geometry    : angle       0.78766 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 174
  time to evaluate  : 1.214 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 CYS cc_start: 0.4824 (m) cc_final: 0.4549 (m)
REVERT: A  253 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6950 (p0)
REVERT: A  343 MET cc_start: 0.8881 (tpt) cc_final: 0.8289 (tpt)
REVERT: A  347 MET cc_start: 0.8757 (mpp) cc_final: 0.7858 (mpp)
REVERT: A  378 MET cc_start: 0.8433 (mpp) cc_final: 0.8122 (mpp)
REVERT: A  689 CYS cc_start: 0.9205 (m) cc_final: 0.8891 (m)
REVERT: B  181 TYR cc_start: 0.9258 (t80) cc_final: 0.8907 (t80)
REVERT: B  195 TYR cc_start: 0.9436 (m-80) cc_final: 0.8928 (m-80)
REVERT: B  210 MET cc_start: 0.8414 (mmm) cc_final: 0.7805 (mmt)
REVERT: B  399 THR cc_start: 0.8300 (m) cc_final: 0.7934 (t)
REVERT: B  441 PHE cc_start: 0.9285 (m-80) cc_final: 0.8961 (m-80)
REVERT: B  450 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8439 (m-30)
REVERT: B  455 PRO cc_start: 0.9641 (Cg_exo) cc_final: 0.8954 (Cg_endo)
REVERT: B  458 ASP cc_start: 0.8888 (OUTLIER) cc_final: 0.8404 (m-30)
REVERT: B  463 HIS cc_start: 0.8915 (m90) cc_final: 0.8464 (m90)
REVERT: C   83 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8667 (mm-40)
REVERT: C   93 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8863 (tt)
REVERT: C  112 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8194 (tp)
REVERT: C  218 TYR cc_start: 0.8935 (OUTLIER) cc_final: 0.7988 (m-10)
  outliers start: 63
  outliers final: 48
  residues processed: 212
  average time/residue: 0.1767
  time to fit residues: 57.4250
Evaluate side-chains
  221 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 166
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  218 PHE
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  537 ILE
Chi-restraints excluded: chain A residue  545 TYR
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  697 LEU
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  381 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  410 CYS
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  450 ASP
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue   62 ARG
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue   93 LEU
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  218 TYR
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 74 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0870
   chunk 67 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 104 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 237 GLN
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.068145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.057649 restraints weight = 48940.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.059300 restraints weight = 27958.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.060389 restraints weight = 18370.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.6113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10033  Z= 0.142
  Angle     :  0.799  14.124  13685  Z= 0.387
  Chirality :  0.045   0.298   1584
  Planarity :  0.005   0.062   1706
  Dihedral  :  5.772  46.859   1354
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.37 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.80 %
    Favored  : 65.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1235
  helix:  1.55 (0.19), residues: 721
  sheet: -2.30 (0.40), residues: 125
  loop : -2.70 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP C 174 
 HIS   0.004   0.001   HIS C  58 
 PHE   0.037   0.002   PHE C 132 
 TYR   0.014   0.001   TYR A 554 
 ARG   0.004   0.000   ARG D  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  594)
  hydrogen bonds       : angle       4.48000 ( 1737)
  SS BOND              : bond        0.00610 (    5)
  SS BOND              : angle       2.17943 (   10)
  covalent geometry    : bond        0.00313 (10028)
  covalent geometry    : angle       0.79684 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 185
  time to evaluate  : 1.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   91 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8853 (p0)
REVERT: A  253 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6875 (p0)
REVERT: A  343 MET cc_start: 0.8894 (tpt) cc_final: 0.8641 (tpt)
REVERT: A  347 MET cc_start: 0.8757 (mpp) cc_final: 0.8358 (mmp)
REVERT: A  378 MET cc_start: 0.8494 (mpp) cc_final: 0.8144 (mpp)
REVERT: A  689 CYS cc_start: 0.9179 (m) cc_final: 0.8833 (m)
REVERT: B  181 TYR cc_start: 0.9246 (t80) cc_final: 0.8904 (t80)
REVERT: B  195 TYR cc_start: 0.9452 (m-80) cc_final: 0.8930 (m-80)
REVERT: B  210 MET cc_start: 0.8492 (mmm) cc_final: 0.8082 (mmt)
REVERT: B  399 THR cc_start: 0.8187 (m) cc_final: 0.7813 (t)
REVERT: B  432 LEU cc_start: 0.6540 (mp) cc_final: 0.6214 (tt)
REVERT: B  450 ASP cc_start: 0.8926 (t70) cc_final: 0.8406 (m-30)
REVERT: B  463 HIS cc_start: 0.8941 (m90) cc_final: 0.8294 (m90)
REVERT: C   22 LEU cc_start: 0.9455 (mm) cc_final: 0.9234 (mm)
REVERT: C   41 PHE cc_start: 0.9074 (m-80) cc_final: 0.8871 (m-10)
REVERT: C   83 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8715 (mm-40)
REVERT: C   86 PHE cc_start: 0.9397 (m-10) cc_final: 0.9188 (t80)
REVERT: C  112 ILE cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (tp)
REVERT: C  218 TYR cc_start: 0.8985 (OUTLIER) cc_final: 0.8005 (m-10)
REVERT: D   20 LEU cc_start: 0.8601 (mt) cc_final: 0.8278 (pp)
  outliers start: 49
  outliers final: 37
  residues processed: 213
  average time/residue: 0.2052
  time to fit residues: 65.9515
Evaluate side-chains
  216 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 174
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  237 GLN
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  545 TYR
Chi-restraints excluded: chain A residue  565 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  458 ASP
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  137 ILE
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  218 TYR
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 33 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 69 optimal weight:   20.0000
   chunk 105 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 512 GLN
** A 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 459 GLN
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.064700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.054511 restraints weight = 51434.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.056017 restraints weight = 29373.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.057119 restraints weight = 19559.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.6102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  10033  Z= 0.281
  Angle     :  0.854  12.791  13685  Z= 0.432
  Chirality :  0.046   0.303   1584
  Planarity :  0.006   0.074   1706
  Dihedral  :  5.937  45.141   1353
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 21.81
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  8.26 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.85 %
    Favored  : 64.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.24), residues: 1235
  helix:  1.31 (0.19), residues: 720
  sheet: -2.10 (0.44), residues: 109
  loop : -2.62 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP C 174 
 HIS   0.009   0.002   HIS A 102 
 PHE   0.032   0.002   PHE C 132 
 TYR   0.020   0.002   TYR A 569 
 ARG   0.005   0.000   ARG D   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  594)
  hydrogen bonds       : angle       4.79418 ( 1737)
  SS BOND              : bond        0.00741 (    5)
  SS BOND              : angle       2.93203 (   10)
  covalent geometry    : bond        0.00601 (10028)
  covalent geometry    : angle       0.85078 (13675)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 170
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  253 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7107 (p0)
REVERT: A  343 MET cc_start: 0.8802 (tpt) cc_final: 0.8319 (tpt)
REVERT: A  347 MET cc_start: 0.8662 (mpp) cc_final: 0.7984 (mpp)
REVERT: A  687 THR cc_start: 0.9497 (m) cc_final: 0.9187 (t)
REVERT: A  689 CYS cc_start: 0.9166 (m) cc_final: 0.8794 (m)
REVERT: B  181 TYR cc_start: 0.9174 (t80) cc_final: 0.8852 (t80)
REVERT: B  195 TYR cc_start: 0.9432 (m-80) cc_final: 0.8916 (m-80)
REVERT: B  210 MET cc_start: 0.8361 (mmm) cc_final: 0.7886 (mmt)
REVERT: B  399 THR cc_start: 0.8355 (m) cc_final: 0.8015 (t)
REVERT: B  441 PHE cc_start: 0.9260 (m-80) cc_final: 0.8722 (m-80)
REVERT: B  463 HIS cc_start: 0.8950 (m90) cc_final: 0.8412 (m90)
REVERT: C   41 PHE cc_start: 0.9047 (m-80) cc_final: 0.8724 (m-10)
REVERT: C   83 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8712 (mm-40)
REVERT: C  112 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: C  205 PHE cc_start: 0.8813 (m-10) cc_final: 0.8582 (m-10)
REVERT: C  218 TYR cc_start: 0.8941 (OUTLIER) cc_final: 0.7947 (m-10)
  outliers start: 45
  outliers final: 38
  residues processed: 195
  average time/residue: 0.1849
  time to fit residues: 54.9787
Evaluate side-chains
  204 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 162
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   91 ASN
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  100 SER
Chi-restraints excluded: chain A residue  102 HIS
Chi-restraints excluded: chain A residue  253 ASP
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  333 GLU
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  545 TYR
Chi-restraints excluded: chain A residue  587 GLN
Chi-restraints excluded: chain A residue  604 TRP
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  631 LEU
Chi-restraints excluded: chain A residue  632 SER
Chi-restraints excluded: chain B residue   80 LYS
Chi-restraints excluded: chain B residue   94 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 LEU
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  388 PHE
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 ASP
Chi-restraints excluded: chain B residue  412 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  452 LEU
Chi-restraints excluded: chain C residue    5 VAL
Chi-restraints excluded: chain C residue    7 PHE
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   67 LEU
Chi-restraints excluded: chain C residue   83 GLN
Chi-restraints excluded: chain C residue  112 ILE
Chi-restraints excluded: chain C residue  114 ILE
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  127 ILE
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain C residue  214 LEU
Chi-restraints excluded: chain C residue  218 TYR
Chi-restraints excluded: chain D residue   71 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 99 optimal weight:    4.9990
   chunk 81 optimal weight:    8.9990
   chunk 114 optimal weight:    8.9990
   chunk 30 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 111 optimal weight:   20.0000
   chunk 13 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 66 optimal weight:    0.6980
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 190 ASN
** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 459 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.066431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.056055 restraints weight = 49703.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.057672 restraints weight = 27857.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.058646 restraints weight = 18129.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.6226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10033  Z= 0.163
  Angle     :  0.815  13.928  13685  Z= 0.395
  Chirality :  0.045   0.308   1584
  Planarity :  0.005   0.064   1706
  Dihedral  :  5.651  41.726   1351
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.61 %
    Favored  : 91.74 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 31.90 %
    Favored  : 64.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.25), residues: 1235
  helix:  1.41 (0.19), residues: 719
  sheet: -2.32 (0.43), residues: 118
  loop : -2.52 (0.32), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP C 174 
 HIS   0.005   0.001   HIS C  58 
 PHE   0.029   0.002   PHE A 302 
 TYR   0.019   0.002   TYR B 225 
 ARG   0.004   0.000   ARG A 371 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  594)
  hydrogen bonds       : angle       4.57491 ( 1737)
  SS BOND              : bond        0.00471 (    5)
  SS BOND              : angle       1.97434 (   10)
  covalent geometry    : bond        0.00367 (10028)
  covalent geometry    : angle       0.81330 (13675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3223.74 seconds
wall clock time: 59 minutes 48.15 seconds (3588.15 seconds total)