Starting phenix.real_space_refine
on Tue Jul 29 20:23:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ri5_24474/07_2025/7ri5_24474.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ri5_24474/07_2025/7ri5_24474.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/7ri5_24474/07_2025/7ri5_24474.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ri5_24474/07_2025/7ri5_24474.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ri5_24474/07_2025/7ri5_24474.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ri5_24474/07_2025/7ri5_24474.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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    7470      2.51       5
     N    2026      2.21       5
     O    2338      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 96 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11866
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 782, 6183
          Classifications: {'peptide': 782}
          Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 750}
    Chain: "B"
      Number of atoms: 2787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2787
          Classifications: {'peptide': 370}
          Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 356}
    Chain: "C"
      Number of atoms: 468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 65, 468
          Classifications: {'peptide': 65}
          Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 56}
    Chain: "D"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Link IDs: {'PTRANS': 12, 'TRANS': 204}
    Chain: "E"
      Number of atoms: 676
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 676
          Classifications: {'peptide': 86}
          Link IDs: {'PTRANS': 5, 'TRANS': 80}
  Time building chain proxies: 6.85, per 1000 atoms: 0.58
  Number of scatterers: 11866
  At special positions: 0
  Unit cell: (102.9, 131.25, 130.2, 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      32     16.00
     O    2338      8.00
     N    2026      7.00
     C    7470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 690 " - pdb=" SG  CYS A 700 " distance=2.04

  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: 2.75
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2780

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 16 sheets defined
      24.4% alpha, 22.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 46
    Processing helix  chain 'A' and resid 55 through 69
      removed outlier: 3.819A  pdb=" N   THR A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 116
    Processing helix  chain 'A' and resid 126 through 145
      removed outlier: 3.590A  pdb=" N   ILE A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ALA A 131 " --> pdb=" O   ARG A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 196
      removed outlier: 4.042A  pdb=" N   HIS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 208
    Processing helix  chain 'A' and resid 215 through 234
    Processing helix  chain 'A' and resid 280 through 288
    Processing helix  chain 'A' and resid 297 through 314
    Processing helix  chain 'A' and resid 361 through 369
      removed outlier: 3.648A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   MET A 369 " --> pdb=" O   LEU A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
    Processing helix  chain 'A' and resid 542 through 553
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'C' and resid 40 through 44
      removed outlier: 3.785A  pdb=" N   ALA C  44 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 46
    Processing helix  chain 'D' and resid 47 through 62
      removed outlier: 3.683A  pdb=" N   TYR D  62 " --> pdb=" O   LEU D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 65 through 83
    Processing helix  chain 'D' and resid 84 through 99
    Processing helix  chain 'D' and resid 104 through 122
    Processing helix  chain 'D' and resid 124 through 129
    Processing helix  chain 'D' and resid 137 through 154
    Processing helix  chain 'D' and resid 159 through 189
    Processing helix  chain 'D' and resid 190 through 205
    Processing helix  chain 'D' and resid 208 through 225
      removed outlier: 3.854A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 242
    Processing helix  chain 'E' and resid 39 through 46
      removed outlier: 4.644A  pdb=" N   ILE E  46 " --> pdb=" O   ASP E  42 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 100
      removed outlier: 3.770A  pdb=" N   LEU A 165 " --> pdb=" O   ALA A  95 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ILE A  97 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   PHE A  99 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   SER A 150 " --> pdb=" O   GLN A 170 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 241 through 248
    Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 276
      removed outlier: 5.000A  pdb=" N   LEU A 268 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   GLY A 270 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 8.061A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   GLU A 272 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 7.356A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 272 " (cutoff:3.500A)
      removed outlier: 5.827A  pdb=" N   SER A 274 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 354
      removed outlier: 6.596A  pdb=" N   ARG A 353 " --> pdb=" O   TYR A 416 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN A 403 " --> pdb=" O   ASP A 413 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 430
      removed outlier: 3.521A  pdb=" N   GLN A 441 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 50
      removed outlier: 3.714A  pdb=" N   THR B  46 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   THR B 391 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 67
      removed outlier: 3.619A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ALA B  83 " --> pdb=" O   TRP B  93 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   TRP B  93 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   ASN B  85 " --> pdb=" O   GLU B  91 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   GLU B  91 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 114 through 118
    Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 157
      removed outlier: 4.823A  pdb=" N   ALA B 173 " --> pdb=" O   TRP B 183 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   TRP B 183 " --> pdb=" O   ALA B 173 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203
      removed outlier: 3.793A  pdb=" N   GLN B 225 " --> pdb=" O   LEU B 220 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254
    Processing sheet with id=AB4, first strand: chain 'B' and resid 288 through 292
      removed outlier: 4.317A  pdb=" N   ASP B 288 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 333
      removed outlier: 3.778A  pdb=" N   ASP B 341 " --> pdb=" O   TYR B 345 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   TYR B 345 " --> pdb=" O   ASP B 341 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 371 through 374
    Processing sheet with id=AB7, first strand: chain 'E' and resid 32 through 34
      removed outlier: 4.205A  pdb=" N   THR E  94 " --> pdb=" O   ASN E 103 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   ASN E 103 " --> pdb=" O   THR E  94 " (cutoff:3.500A)

    522 hydrogen bonds defined for protein.
    1440 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: 3.69

  Time building geometry restraints manager: 3.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3431
        1.33 -     1.45: 2350
        1.45 -     1.58: 6280
        1.58 -     1.70: 1
        1.70 -     1.82: 62
  Bond restraints: 12124
  Sorted by residual:
  bond pdb=" C   ALA B 199 "
       pdb=" N   PRO B 200 "
    ideal  model  delta    sigma   weight residual
    1.333  1.295  0.037 1.17e-02 7.31e+03 1.01e+01
  bond pdb=" CA  THR B 249 "
       pdb=" CB  THR B 249 "
    ideal  model  delta    sigma   weight residual
    1.529  1.487  0.042 1.34e-02 5.57e+03 9.77e+00
  bond pdb=" CA  TYR A 235 "
       pdb=" CB  TYR A 235 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 1.47e-02 4.63e+03 6.58e+00
  bond pdb=" C   LYS B 383 "
       pdb=" N   ASP B 384 "
    ideal  model  delta    sigma   weight residual
    1.331  1.364 -0.033 1.28e-02 6.10e+03 6.46e+00
  bond pdb=" CB  PRO D 100 "
       pdb=" CG  PRO D 100 "
    ideal  model  delta    sigma   weight residual
    1.492  1.611 -0.119 5.00e-02 4.00e+02 5.63e+00
  ... (remaining 12119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.57: 15945
        2.57 -     5.14: 482
        5.14 -     7.71: 49
        7.71 -    10.29: 3
       10.29 -    12.86: 4
  Bond angle restraints: 16483
  Sorted by residual:
  angle pdb=" C   ASN B 350 "
        pdb=" N   VAL B 351 "
        pdb=" CA  VAL B 351 "
      ideal   model   delta    sigma   weight residual
     121.97  133.86  -11.89 1.80e+00 3.09e-01 4.36e+01
  angle pdb=" C   VAL B 351 "
        pdb=" N   GLU B 352 "
        pdb=" CA  GLU B 352 "
      ideal   model   delta    sigma   weight residual
     121.54  132.84  -11.30 1.91e+00 2.74e-01 3.50e+01
  angle pdb=" N   PHE A 478 "
        pdb=" CA  PHE A 478 "
        pdb=" C   PHE A 478 "
      ideal   model   delta    sigma   weight residual
     114.75  107.87    6.88 1.26e+00 6.30e-01 2.99e+01
  angle pdb=" N   ASN B 168 "
        pdb=" CA  ASN B 168 "
        pdb=" C   ASN B 168 "
      ideal   model   delta    sigma   weight residual
     111.87  105.06    6.81 1.41e+00 5.03e-01 2.33e+01
  angle pdb=" CA  PRO D 100 "
        pdb=" N   PRO D 100 "
        pdb=" CD  PRO D 100 "
      ideal   model   delta    sigma   weight residual
     112.00  105.24    6.76 1.40e+00 5.10e-01 2.33e+01
  ... (remaining 16478 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.06: 6470
       18.06 -    36.12: 566
       36.12 -    54.18: 90
       54.18 -    72.24: 19
       72.24 -    90.30: 27
  Dihedral angle restraints: 7172
    sinusoidal: 2799
      harmonic: 4373
  Sorted by residual:
  dihedral pdb=" CA  ILE A 519 "
           pdb=" C   ILE A 519 "
           pdb=" N   ASN A 520 "
           pdb=" CA  ASN A 520 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.26   46.74     0      5.00e+00 4.00e-02 8.74e+01
  dihedral pdb=" CA  GLN E  34 "
           pdb=" C   GLN E  34 "
           pdb=" N   GLY E  35 "
           pdb=" CA  GLY E  35 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.36  -39.64     0      5.00e+00 4.00e-02 6.29e+01
  dihedral pdb=" CA  ALA B 262 "
           pdb=" C   ALA B 262 "
           pdb=" N   TYR B 263 "
           pdb=" CA  TYR B 263 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.86  -37.14     0      5.00e+00 4.00e-02 5.52e+01
  ... (remaining 7169 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1403
       0.062 -    0.124: 357
       0.124 -    0.187: 36
       0.187 -    0.249: 3
       0.249 -    0.311: 1
  Chirality restraints: 1800
  Sorted by residual:
  chirality pdb=" CB  ILE A 519 "
            pdb=" CA  ILE A 519 "
            pdb=" CG1 ILE A 519 "
            pdb=" CG2 ILE A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CB  THR B 328 "
            pdb=" CA  THR B 328 "
            pdb=" OG1 THR B 328 "
            pdb=" CG2 THR B 328 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  TRP A 546 "
            pdb=" N   TRP A 546 "
            pdb=" C   TRP A 546 "
            pdb=" CB  TRP A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1797 not shown)

  Planarity restraints: 2175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  35 "    0.076 5.00e-02 4.00e+02   1.15e-01 2.12e+01
        pdb=" N   PRO B  36 "   -0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO B  36 "    0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO B  36 "    0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 107 "   -0.021 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR D 107 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 107 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 107 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 107 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 107 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 107 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR D 107 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D  99 "   -0.054 5.00e-02 4.00e+02   7.79e-02 9.70e+00
        pdb=" N   PRO D 100 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO D 100 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO D 100 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 2172 not shown)

  Histogram of nonbonded interaction distances:
        1.90 -     2.50: 100
        2.50 -     3.10: 9339
        3.10 -     3.70: 17727
        3.70 -     4.30: 24830
        4.30 -     4.90: 40951
  Nonbonded interactions: 92947
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  35 "
            pdb=" O   VAL E  76 "
     model   vdw
     1.904 3.040
  nonbonded pdb=" O   GLN D  50 "
            pdb=" OG1 THR D  53 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" OH  TYR D 110 "
            pdb=" OD2 ASP D 162 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   GLY D  65 "
            pdb=" OG  SER D  68 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OG1 THR A 423 "
            pdb=" OD1 ASP A 447 "
     model   vdw
     2.155 3.040
  ... (remaining 92942 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:             0.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     28.760
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
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      :  0.007   0.119  12125  Z= 0.342
  Angle     :  1.045  12.858  16485  Z= 0.631
  Chirality :  0.053   0.311   1800
  Planarity :  0.007   0.115   2175
  Dihedral  : 15.004  90.297   4389
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 22.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.05 %
    Favored  : 86.75 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  0.71 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.74 (0.20), residues: 1510
  helix:  0.44 (0.27), residues: 334
  sheet: -1.73 (0.24), residues: 400
  loop : -2.99 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP B 228 
 HIS   0.008   0.002   HIS A 280 
 PHE   0.023   0.002   PHE A 490 
 TYR   0.058   0.003   TYR D 107 
 ARG   0.022   0.001   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11546 (  522)
  hydrogen bonds       : angle       7.11473 ( 1440)
  SS BOND              : bond        0.00564 (    1)
  SS BOND              : angle       0.97987 (    2)
  covalent geometry    : bond        0.00717 (12124)
  covalent geometry    : angle       1.04460 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 241
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ASP cc_start: 0.7556 (m-30) cc_final: 0.7324 (m-30)
REVERT: A  252 LYS cc_start: 0.7507 (mttt) cc_final: 0.7171 (pttt)
REVERT: A  358 ASP cc_start: 0.8395 (m-30) cc_final: 0.8166 (t0)
REVERT: A  661 ARG cc_start: 0.6978 (mpp-170) cc_final: 0.6512 (mtm-85)
REVERT: A  725 ILE cc_start: 0.3401 (pt) cc_final: 0.3164 (pt)
REVERT: A  741 MET cc_start: 0.8623 (ptm) cc_final: 0.8275 (ptt)
REVERT: A  777 MET cc_start: 0.7210 (ptm) cc_final: 0.6415 (tpp)
REVERT: B   32 MET cc_start: 0.8321 (mpp) cc_final: 0.7955 (mmm)
REVERT: B  215 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7510 (tpt90)
REVERT: B  392 ARG cc_start: 0.6500 (mpt180) cc_final: 0.5782 (mmt-90)
REVERT: C   73 SER cc_start: 0.8015 (p) cc_final: 0.7787 (p)
  outliers start: 4
  outliers final: 1
  residues processed: 244
  average time/residue: 0.2227
  time to fit residues: 79.4169
Evaluate side-chains
  199 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.9980
   chunk 113 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 117 optimal weight:   20.0000
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 136 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 170 GLN
B 172 GLN
B 186 ASN
B 368 GLN
D 230 GLN
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.185168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.152762 restraints weight = 17831.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.151562 restraints weight = 20719.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.153085 restraints weight = 20334.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12125  Z= 0.166
  Angle     :  0.767  12.621  16485  Z= 0.411
  Chirality :  0.048   0.203   1800
  Planarity :  0.006   0.082   2175
  Dihedral  :  7.092  43.334   1669
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.06 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.29 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.52 (0.21), residues: 1510
  helix:  0.63 (0.28), residues: 345
  sheet: -1.61 (0.24), residues: 400
  loop : -2.90 (0.20), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 279 
 HIS   0.006   0.001   HIS A 280 
 PHE   0.014   0.001   PHE A 490 
 TYR   0.029   0.002   TYR C  41 
 ARG   0.008   0.001   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04646 (  522)
  hydrogen bonds       : angle       6.27810 ( 1440)
  SS BOND              : bond        0.00333 (    1)
  SS BOND              : angle       0.53632 (    2)
  covalent geometry    : bond        0.00355 (12124)
  covalent geometry    : angle       0.76681 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 1.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 THR cc_start: 0.7309 (p) cc_final: 0.7103 (p)
REVERT: A  232 ASP cc_start: 0.7456 (m-30) cc_final: 0.7233 (m-30)
REVERT: A  252 LYS cc_start: 0.7364 (mttt) cc_final: 0.7090 (pttt)
REVERT: A  262 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8174 (mm-30)
REVERT: A  725 ILE cc_start: 0.3402 (pt) cc_final: 0.3165 (pt)
REVERT: A  777 MET cc_start: 0.7068 (ptm) cc_final: 0.6162 (tpp)
REVERT: B  215 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7583 (tpt90)
REVERT: B  392 ARG cc_start: 0.6149 (mpt180) cc_final: 0.5733 (mmt-90)
REVERT: C   73 SER cc_start: 0.7993 (p) cc_final: 0.7782 (p)
REVERT: D   79 TYR cc_start: 0.8827 (m-10) cc_final: 0.8332 (m-10)
REVERT: D   84 ASP cc_start: 0.8226 (m-30) cc_final: 0.7660 (p0)
  outliers start: 20
  outliers final: 13
  residues processed: 228
  average time/residue: 0.2228
  time to fit residues: 74.8808
Evaluate side-chains
  208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 195
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  563 ASN
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain B residue  292 ASP
Chi-restraints excluded: chain D residue  211 THR
Chi-restraints excluded: chain E residue   50 MET
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   90 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 116 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 65 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 301 GLN
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 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 = 0.4142 r_free = 0.4142 target = 0.182002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.149183 restraints weight = 18196.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.148051 restraints weight = 22737.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.149547 restraints weight = 21943.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  12125  Z= 0.209
  Angle     :  0.763  11.640  16485  Z= 0.406
  Chirality :  0.047   0.242   1800
  Planarity :  0.005   0.068   2175
  Dihedral  :  6.880  42.526   1669
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.05 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 14.14 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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: -2.41 (0.21), residues: 1510
  helix:  0.75 (0.27), residues: 347
  sheet: -1.48 (0.25), residues: 390
  loop : -2.89 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 279 
 HIS   0.004   0.001   HIS B 165 
 PHE   0.020   0.002   PHE A 738 
 TYR   0.034   0.002   TYR C  41 
 ARG   0.010   0.001   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04477 (  522)
  hydrogen bonds       : angle       6.08435 ( 1440)
  SS BOND              : bond        0.00377 (    1)
  SS BOND              : angle       0.72557 (    2)
  covalent geometry    : bond        0.00461 (12124)
  covalent geometry    : angle       0.76302 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 207
  time to evaluate  : 1.218 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 ASP cc_start: 0.7180 (m-30) cc_final: 0.6936 (m-30)
REVERT: A  450 LEU cc_start: 0.5344 (OUTLIER) cc_final: 0.4995 (pp)
REVERT: A  641 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6701 (pp)
REVERT: A  719 ILE cc_start: 0.8033 (mp) cc_final: 0.7787 (mp)
REVERT: A  777 MET cc_start: 0.7022 (ptm) cc_final: 0.5820 (tpt)
REVERT: B  215 ARG cc_start: 0.7821 (mmm160) cc_final: 0.7513 (tpt90)
REVERT: B  308 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6714 (mt)
REVERT: B  392 ARG cc_start: 0.6407 (mpt180) cc_final: 0.5749 (mmt-90)
REVERT: C   73 SER cc_start: 0.8000 (p) cc_final: 0.7758 (p)
REVERT: D   84 ASP cc_start: 0.8298 (m-30) cc_final: 0.7882 (p0)
REVERT: E   66 ASP cc_start: 0.8129 (t0) cc_final: 0.7839 (t0)
  outliers start: 30
  outliers final: 18
  residues processed: 228
  average time/residue: 0.2103
  time to fit residues: 70.9445
Evaluate side-chains
  220 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 199
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain E residue   50 MET
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   90 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 102 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 120 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 140 optimal weight:    1.9990
   chunk 84 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 108 optimal weight:    5.9990
   chunk 56 optimal weight:    5.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.178288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.145441 restraints weight = 18208.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.142904 restraints weight = 22762.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.144343 restraints weight = 22303.222|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12125  Z= 0.280
  Angle     :  0.801  12.135  16485  Z= 0.427
  Chirality :  0.049   0.199   1800
  Planarity :  0.006   0.062   2175
  Dihedral  :  7.076  43.922   1669
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 15.83
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.85 %
    Favored  : 86.95 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 14.77 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

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: -2.48 (0.21), residues: 1510
  helix:  0.69 (0.27), residues: 346
  sheet: -1.60 (0.24), residues: 393
  loop : -2.87 (0.20), residues: 771

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 206 
 HIS   0.006   0.001   HIS B 165 
 PHE   0.023   0.002   PHE A 169 
 TYR   0.029   0.002   TYR C  41 
 ARG   0.010   0.001   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04638 (  522)
  hydrogen bonds       : angle       6.19038 ( 1440)
  SS BOND              : bond        0.00436 (    1)
  SS BOND              : angle       0.97452 (    2)
  covalent geometry    : bond        0.00623 (12124)
  covalent geometry    : angle       0.80099 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 201
  time to evaluate  : 1.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8477 (tp40) cc_final: 0.8269 (tp40)
REVERT: A  230 TYR cc_start: 0.8749 (m-80) cc_final: 0.8185 (m-80)
REVERT: A  373 GLU cc_start: 0.8078 (tt0) cc_final: 0.7858 (tt0)
REVERT: A  450 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.5234 (mp)
REVERT: A  546 TRP cc_start: 0.7942 (OUTLIER) cc_final: 0.7627 (m-90)
REVERT: A  549 LEU cc_start: 0.8413 (mm) cc_final: 0.8044 (mm)
REVERT: A  641 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6775 (pp)
REVERT: A  777 MET cc_start: 0.7168 (ptm) cc_final: 0.6077 (tpt)
REVERT: B  215 ARG cc_start: 0.7928 (mmm160) cc_final: 0.7473 (tpt90)
REVERT: B  306 MET cc_start: 0.6983 (tmm) cc_final: 0.6528 (tmm)
REVERT: B  308 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6820 (mt)
REVERT: C   73 SER cc_start: 0.8090 (p) cc_final: 0.7849 (p)
REVERT: D   84 ASP cc_start: 0.8418 (m-30) cc_final: 0.8039 (p0)
REVERT: D  111 MET cc_start: 0.9266 (mmm) cc_final: 0.9014 (tpp)
REVERT: E   66 ASP cc_start: 0.8309 (t0) cc_final: 0.7885 (t0)
  outliers start: 43
  outliers final: 29
  residues processed: 233
  average time/residue: 0.2174
  time to fit residues: 74.4058
Evaluate side-chains
  220 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 187
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  169 PHE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   50 MET
Chi-restraints excluded: chain E residue   68 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 6 optimal weight:    7.9990
   chunk 145 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0570
   chunk 10 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** 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 = 0.4180 r_free = 0.4180 target = 0.185199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.154389 restraints weight = 18058.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.153844 restraints weight = 21091.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.155004 restraints weight = 21489.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12125  Z= 0.136
  Angle     :  0.698  10.576  16485  Z= 0.368
  Chirality :  0.046   0.169   1800
  Planarity :  0.005   0.054   2175
  Dihedral  :  6.343  39.992   1669
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.26 %
    Favored  : 89.60 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.75 %
    Favored  : 79.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.31 (0.21), residues: 1510
  helix:  0.92 (0.27), residues: 349
  sheet: -1.47 (0.25), residues: 385
  loop : -2.84 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 279 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.019   0.001   PHE A 738 
 TYR   0.022   0.001   TYR D 184 
 ARG   0.006   0.001   ARG B 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04041 (  522)
  hydrogen bonds       : angle       5.81219 ( 1440)
  SS BOND              : bond        0.00256 (    1)
  SS BOND              : angle       0.32136 (    2)
  covalent geometry    : bond        0.00292 (12124)
  covalent geometry    : angle       0.69802 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 207
  time to evaluate  : 1.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8300 (tp40) cc_final: 0.8066 (tp40)
REVERT: A  230 TYR cc_start: 0.8637 (m-80) cc_final: 0.8310 (m-80)
REVERT: A  368 GLU cc_start: 0.7163 (tp30) cc_final: 0.6580 (tp30)
REVERT: A  421 ARG cc_start: 0.7025 (ptt180) cc_final: 0.6672 (tmm160)
REVERT: A  450 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4778 (mp)
REVERT: A  485 LEU cc_start: 0.8561 (tp) cc_final: 0.8356 (tt)
REVERT: A  549 LEU cc_start: 0.8316 (mm) cc_final: 0.7982 (mm)
REVERT: A  641 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6540 (pp)
REVERT: A  777 MET cc_start: 0.6676 (ptm) cc_final: 0.5705 (tpt)
REVERT: B  215 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7492 (tpt90)
REVERT: B  306 MET cc_start: 0.6751 (tmm) cc_final: 0.6363 (tmm)
REVERT: B  308 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6553 (mt)
REVERT: C   43 GLU cc_start: 0.8473 (mp0) cc_final: 0.7870 (mp0)
REVERT: C   73 SER cc_start: 0.7937 (p) cc_final: 0.7713 (p)
REVERT: D   84 ASP cc_start: 0.8280 (m-30) cc_final: 0.7802 (p0)
REVERT: D  111 MET cc_start: 0.9188 (mmm) cc_final: 0.8874 (tpp)
REVERT: E   66 ASP cc_start: 0.8121 (t0) cc_final: 0.7786 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 229
  average time/residue: 0.2265
  time to fit residues: 76.0371
Evaluate side-chains
  211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   68 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 131 optimal weight:    6.9990
   chunk 89 optimal weight:    6.9990
   chunk 143 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 115 optimal weight:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 GLN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** 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 = 0.4098 r_free = 0.4098 target = 0.177461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.146746 restraints weight = 18279.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.147031 restraints weight = 24968.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.148143 restraints weight = 23366.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072  12125  Z= 0.280
  Angle     :  0.793   8.846  16485  Z= 0.424
  Chirality :  0.049   0.229   1800
  Planarity :  0.006   0.054   2175
  Dihedral  :  6.780  41.942   1669
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.85 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.12 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.41 (0.21), residues: 1510
  helix:  0.86 (0.28), residues: 346
  sheet: -1.58 (0.25), residues: 397
  loop : -2.89 (0.20), residues: 767

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 546 
 HIS   0.005   0.001   HIS B 165 
 PHE   0.025   0.002   PHE A 169 
 TYR   0.023   0.002   TYR C  41 
 ARG   0.009   0.001   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04578 (  522)
  hydrogen bonds       : angle       6.04432 ( 1440)
  SS BOND              : bond        0.00366 (    1)
  SS BOND              : angle       0.79462 (    2)
  covalent geometry    : bond        0.00626 (12124)
  covalent geometry    : angle       0.79305 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 195
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8397 (tp40) cc_final: 0.8190 (tp40)
REVERT: A  230 TYR cc_start: 0.8751 (m-80) cc_final: 0.8485 (m-80)
REVERT: A  262 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7783 (mm-30)
REVERT: A  421 ARG cc_start: 0.7346 (ptt180) cc_final: 0.6867 (tmm160)
REVERT: A  450 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5307 (mt)
REVERT: A  549 LEU cc_start: 0.8342 (mm) cc_final: 0.8004 (mm)
REVERT: A  641 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6714 (pp)
REVERT: A  719 ILE cc_start: 0.8191 (mp) cc_final: 0.7809 (mt)
REVERT: A  741 MET cc_start: 0.8685 (ptm) cc_final: 0.8457 (ptt)
REVERT: A  777 MET cc_start: 0.7065 (ptm) cc_final: 0.6085 (tpt)
REVERT: A  789 GLN cc_start: 0.8202 (tp40) cc_final: 0.7449 (pt0)
REVERT: B  215 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7574 (tpt90)
REVERT: C   73 SER cc_start: 0.7992 (p) cc_final: 0.7755 (p)
REVERT: D   84 ASP cc_start: 0.8356 (m-30) cc_final: 0.7897 (p0)
REVERT: D   99 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7861 (p0)
REVERT: D  111 MET cc_start: 0.9273 (mmm) cc_final: 0.8966 (tpp)
REVERT: E   66 ASP cc_start: 0.8277 (t0) cc_final: 0.7888 (t0)
  outliers start: 47
  outliers final: 35
  residues processed: 226
  average time/residue: 0.2125
  time to fit residues: 71.5448
Evaluate side-chains
  229 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 191
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  169 PHE
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  609 TYR
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  124 ILE
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  266 ASN
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain C residue   71 ASN
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   68 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 139 optimal weight:    0.9980
   chunk 2 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 142 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.183856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.152419 restraints weight = 18249.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.151300 restraints weight = 22279.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.152917 restraints weight = 20304.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  12125  Z= 0.147
  Angle     :  0.707   8.931  16485  Z= 0.372
  Chirality :  0.046   0.250   1800
  Planarity :  0.005   0.048   2175
  Dihedral  :  6.262  39.420   1669
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.46 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.09 %
    Favored  : 78.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.32 (0.21), residues: 1510
  helix:  0.94 (0.27), residues: 348
  sheet: -1.48 (0.25), residues: 386
  loop : -2.85 (0.20), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.023   0.001   PHE A 738 
 TYR   0.019   0.001   TYR D 184 
 ARG   0.006   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  522)
  hydrogen bonds       : angle       5.73654 ( 1440)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.47536 (    2)
  covalent geometry    : bond        0.00322 (12124)
  covalent geometry    : angle       0.70699 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 201
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8345 (tp40) cc_final: 0.8116 (tp40)
REVERT: A  230 TYR cc_start: 0.8602 (m-80) cc_final: 0.8319 (m-80)
REVERT: A  368 GLU cc_start: 0.7575 (tp30) cc_final: 0.6889 (tp30)
REVERT: A  421 ARG cc_start: 0.7066 (ptt180) cc_final: 0.6670 (tmm160)
REVERT: A  450 LEU cc_start: 0.5223 (OUTLIER) cc_final: 0.4900 (mt)
REVERT: A  549 LEU cc_start: 0.8297 (mm) cc_final: 0.7962 (mm)
REVERT: A  641 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6553 (pp)
REVERT: A  661 ARG cc_start: 0.6691 (mpp-170) cc_final: 0.6217 (mtm180)
REVERT: A  719 ILE cc_start: 0.8098 (mp) cc_final: 0.7703 (mt)
REVERT: A  777 MET cc_start: 0.6735 (ptm) cc_final: 0.5887 (tpt)
REVERT: A  789 GLN cc_start: 0.8142 (tp40) cc_final: 0.7412 (pt0)
REVERT: B  215 ARG cc_start: 0.7839 (mmm160) cc_final: 0.7498 (tpt90)
REVERT: B  306 MET cc_start: 0.6823 (tmm) cc_final: 0.6203 (tmm)
REVERT: C   43 GLU cc_start: 0.8436 (mp0) cc_final: 0.7749 (mp0)
REVERT: C   73 SER cc_start: 0.7964 (p) cc_final: 0.7738 (p)
REVERT: D   84 ASP cc_start: 0.8346 (m-30) cc_final: 0.7782 (p0)
REVERT: D   99 ASN cc_start: 0.8348 (OUTLIER) cc_final: 0.7902 (p0)
REVERT: D  111 MET cc_start: 0.9200 (mmm) cc_final: 0.8847 (tpp)
REVERT: E   66 ASP cc_start: 0.8087 (t0) cc_final: 0.7726 (t0)
  outliers start: 29
  outliers final: 21
  residues processed: 220
  average time/residue: 0.2108
  time to fit residues: 68.7746
Evaluate side-chains
  210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   68 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 139 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 64 optimal weight:   10.0000
   chunk 140 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   chunk 108 optimal weight:    0.0170
   chunk 85 optimal weight:    7.9990
   chunk 13 optimal weight:   20.0000
   chunk 46 optimal weight:    9.9990
   overall best weight:    0.6622

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 561 GLN
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 230 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.186878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.156422 restraints weight = 18251.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.155993 restraints weight = 22681.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.156999 restraints weight = 20272.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7192
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  12125  Z= 0.130
  Angle     :  0.697  10.062  16485  Z= 0.363
  Chirality :  0.045   0.218   1800
  Planarity :  0.005   0.044   2175
  Dihedral  :  5.974  36.968   1669
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 13.17
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.73 %
    Favored  : 89.21 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 19.72 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.19 (0.21), residues: 1510
  helix:  1.00 (0.27), residues: 349
  sheet: -1.39 (0.25), residues: 388
  loop : -2.76 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 546 
 HIS   0.003   0.000   HIS B 347 
 PHE   0.024   0.001   PHE D  64 
 TYR   0.020   0.001   TYR D 184 
 ARG   0.006   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03810 (  522)
  hydrogen bonds       : angle       5.52159 ( 1440)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.18908 (    2)
  covalent geometry    : bond        0.00284 (12124)
  covalent geometry    : angle       0.69743 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 205
  time to evaluate  : 1.645 
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: A  177 ILE cc_start: 0.5540 (OUTLIER) cc_final: 0.4871 (pt)
REVERT: A  217 GLN cc_start: 0.8172 (tp40) cc_final: 0.7925 (tp40)
REVERT: A  450 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4779 (mt)
REVERT: A  549 LEU cc_start: 0.8215 (mm) cc_final: 0.7841 (mm)
REVERT: A  641 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6555 (pp)
REVERT: A  719 ILE cc_start: 0.8029 (mp) cc_final: 0.7570 (mt)
REVERT: A  777 MET cc_start: 0.6503 (ptm) cc_final: 0.5363 (tpt)
REVERT: C   43 GLU cc_start: 0.8401 (mp0) cc_final: 0.7762 (mp0)
REVERT: C   73 SER cc_start: 0.7906 (p) cc_final: 0.7673 (p)
REVERT: D   84 ASP cc_start: 0.8316 (m-30) cc_final: 0.7687 (p0)
REVERT: D   99 ASN cc_start: 0.8291 (OUTLIER) cc_final: 0.7862 (p0)
REVERT: E   66 ASP cc_start: 0.7989 (t0) cc_final: 0.7650 (t0)
  outliers start: 30
  outliers final: 17
  residues processed: 225
  average time/residue: 0.2594
  time to fit residues: 87.3793
Evaluate side-chains
  213 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 148 optimal weight:    4.9990
   chunk 65 optimal weight:   10.0000
   chunk 112 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 118 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 51 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 142 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 241 ASN
** E  36 ASN ** 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 = 0.4171 r_free = 0.4171 target = 0.184037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.153456 restraints weight = 18233.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.153761 restraints weight = 22040.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.155381 restraints weight = 20065.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7221
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12125  Z= 0.172
  Angle     :  0.720   9.982  16485  Z= 0.376
  Chirality :  0.046   0.179   1800
  Planarity :  0.005   0.045   2175
  Dihedral  :  6.093  37.842   1669
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.66 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.80 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

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: -2.19 (0.21), residues: 1510
  helix:  1.08 (0.27), residues: 346
  sheet: -1.59 (0.25), residues: 403
  loop : -2.68 (0.21), residues: 761

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 348 
 HIS   0.003   0.001   HIS B 347 
 PHE   0.018   0.001   PHE A 490 
 TYR   0.019   0.002   TYR A 477 
 ARG   0.008   0.001   ARG A 367 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03892 (  522)
  hydrogen bonds       : angle       5.58508 ( 1440)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       0.47516 (    2)
  covalent geometry    : bond        0.00383 (12124)
  covalent geometry    : angle       0.71997 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 188
  time to evaluate  : 1.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.3847 (OUTLIER) cc_final: 0.3200 (pmm)
REVERT: A  217 GLN cc_start: 0.8237 (tp40) cc_final: 0.7982 (tp40)
REVERT: A  261 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8063 (p)
REVERT: A  450 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4962 (mt)
REVERT: A  549 LEU cc_start: 0.8203 (mm) cc_final: 0.7801 (mm)
REVERT: A  641 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6536 (pp)
REVERT: A  719 ILE cc_start: 0.8051 (mp) cc_final: 0.7615 (mt)
REVERT: A  777 MET cc_start: 0.6507 (ptm) cc_final: 0.5580 (tpt)
REVERT: A  789 GLN cc_start: 0.7988 (mm110) cc_final: 0.7172 (pt0)
REVERT: B   48 TRP cc_start: 0.6866 (OUTLIER) cc_final: 0.6513 (t60)
REVERT: C   43 GLU cc_start: 0.8401 (mp0) cc_final: 0.7810 (mp0)
REVERT: C   73 SER cc_start: 0.7926 (p) cc_final: 0.7670 (p)
REVERT: C   80 LEU cc_start: 0.8226 (pt) cc_final: 0.7974 (pp)
REVERT: D   84 ASP cc_start: 0.8359 (m-30) cc_final: 0.7717 (p0)
REVERT: E   66 ASP cc_start: 0.8026 (t0) cc_final: 0.7708 (t0)
  outliers start: 35
  outliers final: 25
  residues processed: 212
  average time/residue: 0.2770
  time to fit residues: 88.1311
Evaluate side-chains
  211 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   48 TRP
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain B residue  228 TRP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain C residue   67 ILE
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue   71 VAL
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 8 optimal weight:    0.0870
   chunk 43 optimal weight:    0.9980
   chunk 149 optimal weight:    4.9990
   chunk 132 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 101 optimal weight:    0.1980
   chunk 5 optimal weight:    9.9990
   chunk 61 optimal weight:   10.0000
   chunk 125 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.187174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.156300 restraints weight = 18142.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155464 restraints weight = 23238.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157270 restraints weight = 20218.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12125  Z= 0.135
  Angle     :  0.705   8.824  16485  Z= 0.370
  Chirality :  0.045   0.168   1800
  Planarity :  0.005   0.051   2175
  Dihedral  :  5.890  36.942   1669
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.60 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.50 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -2.10 (0.21), residues: 1510
  helix:  1.09 (0.27), residues: 348
  sheet: -1.50 (0.25), residues: 405
  loop : -2.62 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 546 
 HIS   0.004   0.000   HIS B 347 
 PHE   0.025   0.001   PHE D  64 
 TYR   0.016   0.001   TYR E  57 
 ARG   0.010   0.001   ARG C  33 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03708 (  522)
  hydrogen bonds       : angle       5.46410 ( 1440)
  SS BOND              : bond        0.00173 (    1)
  SS BOND              : angle       0.29404 (    2)
  covalent geometry    : bond        0.00299 (12124)
  covalent geometry    : angle       0.70523 (16483)

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

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

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3020 Ramachandran restraints generated.
    1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 184
  time to evaluate  : 1.958 
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: A   46 MET cc_start: 0.3757 (OUTLIER) cc_final: 0.3133 (pmm)
REVERT: A  177 ILE cc_start: 0.5536 (OUTLIER) cc_final: 0.4822 (pt)
REVERT: A  217 GLN cc_start: 0.8256 (tp40) cc_final: 0.8026 (tp40)
REVERT: A  261 THR cc_start: 0.8209 (OUTLIER) cc_final: 0.7880 (p)
REVERT: A  367 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6203 (tpp80)
REVERT: A  450 LEU cc_start: 0.5215 (OUTLIER) cc_final: 0.4865 (mt)
REVERT: A  549 LEU cc_start: 0.8246 (mm) cc_final: 0.7852 (mm)
REVERT: A  619 VAL cc_start: 0.7990 (t) cc_final: 0.7617 (m)
REVERT: A  641 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6435 (pp)
REVERT: A  719 ILE cc_start: 0.8014 (mp) cc_final: 0.7562 (mt)
REVERT: A  777 MET cc_start: 0.6326 (ptm) cc_final: 0.5376 (tpt)
REVERT: A  789 GLN cc_start: 0.8000 (mm110) cc_final: 0.7115 (pt0)
REVERT: C   43 GLU cc_start: 0.8387 (mp0) cc_final: 0.7905 (mp0)
REVERT: C   73 SER cc_start: 0.7863 (p) cc_final: 0.7620 (p)
REVERT: C   80 LEU cc_start: 0.8332 (pt) cc_final: 0.8132 (pp)
REVERT: D   84 ASP cc_start: 0.8375 (m-30) cc_final: 0.7718 (p0)
REVERT: E   66 ASP cc_start: 0.7895 (t0) cc_final: 0.7585 (t0)
  outliers start: 32
  outliers final: 23
  residues processed: 202
  average time/residue: 0.3003
  time to fit residues: 88.8677
Evaluate side-chains
  208 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 180
  time to evaluate  : 1.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  177 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  308 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  515 LEU
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  228 TRP
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain D residue   59 ASP
Chi-restraints excluded: chain D residue  119 LEU
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   68 PHE
Chi-restraints excluded: chain E residue   72 THR
Chi-restraints excluded: chain E residue   93 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 114 optimal weight:    7.9990
   chunk 102 optimal weight:    9.9990
   chunk 139 optimal weight:    0.0270
   chunk 35 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 106 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 345 ASN
** A 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 223 GLN
E  41 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.189589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.159030 restraints weight = 18237.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.158397 restraints weight = 22474.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.159500 restraints weight = 20026.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12125  Z= 0.125
  Angle     :  0.683   8.786  16485  Z= 0.357
  Chirality :  0.044   0.172   1800
  Planarity :  0.005   0.056   2175
  Dihedral  :  5.678  37.664   1669
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.13 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.58 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -1.94 (0.21), residues: 1510
  helix:  1.23 (0.27), residues: 348
  sheet: -1.38 (0.25), residues: 405
  loop : -2.53 (0.21), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 546 
 HIS   0.004   0.000   HIS B 347 
 PHE   0.015   0.001   PHE A 490 
 TYR   0.017   0.001   TYR A 531 
 ARG   0.006   0.000   ARG D 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03612 (  522)
  hydrogen bonds       : angle       5.34401 ( 1440)
  SS BOND              : bond        0.00148 (    1)
  SS BOND              : angle       0.20241 (    2)
  covalent geometry    : bond        0.00277 (12124)
  covalent geometry    : angle       0.68272 (16483)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3688.44 seconds
wall clock time: 67 minutes 30.32 seconds (4050.32 seconds total)