Starting phenix.real_space_refine
on Wed Mar  4 06:52:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ri5_24474/03_2026/7ri5_24474.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ri5_24474/03_2026/7ri5_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_24474/03_2026/7ri5_24474.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ri5_24474/03_2026/7ri5_24474.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ri5_24474/03_2026/7ri5_24474.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ri5_24474/03_2026/7ri5_24474.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.53, per 1000 atoms: 0.21
  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: 0.90
  Conformation dependent library (CDL) restraints added in 538.7 milliseconds
  

  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: 0.38
  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: 1.86

  Time building geometry restraints manager: 1.24 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:             0.490
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.530
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.620
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.74 (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
 ARG   0.022   0.001   ARG D 166 
 TYR   0.058   0.003   TYR D 107 
 PHE   0.023   0.002   PHE A 490 
 TRP   0.031   0.004   TRP B 228 
 HIS   0.008   0.002   HIS A 280 

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

*********************** 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  : 0.426 
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: 0.7170 (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: 0.7897 (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: 0.1016
  time to fit residues: 36.5579
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  : 0.444 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    2.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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
** C  71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.183970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.151271 restraints weight = 17992.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.149659 restraints weight = 21911.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151455 restraints weight = 19952.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.152063 restraints weight = 14358.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.152393 restraints weight = 13187.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.1381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12125  Z= 0.181
  Angle     :  0.776  12.735  16485  Z= 0.416
  Chirality :  0.048   0.202   1800
  Planarity :  0.006   0.083   2175
  Dihedral  :  7.148  43.554   1669
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 16.09
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.59 %
    Favored  : 88.21 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.68 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.54 (0.21), residues: 1510
  helix:  0.62 (0.28), residues: 345
  sheet: -1.63 (0.24), residues: 400
  loop : -2.91 (0.20), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 355 
 TYR   0.032   0.002   TYR C  41 
 PHE   0.015   0.002   PHE A 490 
 TRP   0.020   0.002   TRP B 279 
 HIS   0.006   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12124)
  covalent geometry    : angle       0.77555 (16483)
  SS BOND              : bond        0.00358 (    1)
  SS BOND              : angle       0.59304 (    2)
  hydrogen bonds       : bond        0.04638 (  522)
  hydrogen bonds       : angle       6.30362 ( 1440)

*********************** 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
  242 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  252 LYS cc_start: 0.7369 (mttt) cc_final: 0.7115 (pttt)
REVERT: A  262 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8188 (mm-30)
REVERT: A  661 ARG cc_start: 0.6951 (mpp-170) cc_final: 0.6311 (mtm-85)
REVERT: A  777 MET cc_start: 0.7080 (ptm) cc_final: 0.6190 (tpp)
REVERT: B  215 ARG cc_start: 0.7789 (mmm160) cc_final: 0.7567 (tpt90)
REVERT: C   73 SER cc_start: 0.7983 (p) cc_final: 0.7762 (p)
REVERT: D   79 TYR cc_start: 0.8835 (m-10) cc_final: 0.8348 (m-10)
REVERT: D   84 ASP cc_start: 0.8203 (m-30) cc_final: 0.7784 (p0)
  outliers start: 21
  outliers final: 13
  residues processed: 230
  average time/residue: 0.1027
  time to fit residues: 34.7702
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  : 0.474 
-------------------------------------------------------------------------------
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 16 optimal weight:    8.9990
   chunk 106 optimal weight:    8.9990
   chunk 148 optimal weight:    9.9990
   chunk 147 optimal weight:    0.6980
   chunk 9 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 99 optimal weight:   10.0000
   chunk 1 optimal weight:   30.0000
   chunk 125 optimal weight:    6.9990
   chunk 137 optimal weight:    0.7980
   overall best weight:    2.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.180152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.146161 restraints weight = 18179.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.144273 restraints weight = 21089.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.145672 restraints weight = 21091.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.146464 restraints weight = 15439.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.146669 restraints weight = 14946.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  12125  Z= 0.241
  Angle     :  0.788  11.643  16485  Z= 0.421
  Chirality :  0.048   0.219   1800
  Planarity :  0.006   0.069   2175
  Dihedral  :  7.040  43.126   1669
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 15.92
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 12.52 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 14.61 %
    Favored  : 82.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.21), residues: 1510
  helix:  0.68 (0.27), residues: 346
  sheet: -1.55 (0.24), residues: 396
  loop : -2.90 (0.20), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 346 
 TYR   0.034   0.002   TYR C  41 
 PHE   0.018   0.002   PHE A 490 
 TRP   0.018   0.003   TRP A 449 
 HIS   0.005   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 (12124)
  covalent geometry    : angle       0.78789 (16483)
  SS BOND              : bond        0.00409 (    1)
  SS BOND              : angle       0.85399 (    2)
  hydrogen bonds       : bond        0.04636 (  522)
  hydrogen bonds       : angle       6.18055 ( 1440)

*********************** 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
  239 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 208
  time to evaluate  : 0.458 
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  450 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.5164 (pp)
REVERT: A  549 LEU cc_start: 0.8406 (mm) cc_final: 0.8053 (mm)
REVERT: A  641 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6661 (pp)
REVERT: A  719 ILE cc_start: 0.8085 (mp) cc_final: 0.7842 (mp)
REVERT: A  777 MET cc_start: 0.6985 (ptm) cc_final: 0.5858 (tpt)
REVERT: B  215 ARG cc_start: 0.7864 (mmm160) cc_final: 0.7454 (tpt90)
REVERT: B  308 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6765 (mt)
REVERT: C   73 SER cc_start: 0.8017 (p) cc_final: 0.7755 (p)
REVERT: D   84 ASP cc_start: 0.8337 (m-30) cc_final: 0.7891 (p0)
REVERT: D  205 TYR cc_start: 0.8781 (OUTLIER) cc_final: 0.8449 (p90)
REVERT: E   66 ASP cc_start: 0.8232 (t0) cc_final: 0.7935 (t0)
  outliers start: 31
  outliers final: 19
  residues processed: 228
  average time/residue: 0.0989
  time to fit residues: 34.0218
Evaluate side-chains
  213 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 190
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
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  641 LEU
Chi-restraints excluded: chain B residue  153 SER
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  352 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain D residue  205 TYR
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 146 optimal weight:    0.5980
   chunk 145 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 24 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 93 optimal weight:    3.9990
   chunk 120 optimal weight:    7.9990
   chunk 133 optimal weight:    2.9990
   chunk 25 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 520 ASN
A 561 GLN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.179110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.145230 restraints weight = 18146.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.142539 restraints weight = 21435.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.144087 restraints weight = 21593.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.144932 restraints weight = 15499.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.145230 restraints weight = 14750.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1984

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= 0.238
  Angle     :  0.773  11.927  16485  Z= 0.412
  Chirality :  0.048   0.248   1800
  Planarity :  0.005   0.061   2175
  Dihedral  :  6.962  42.960   1669
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.72 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 15.24 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.20), residues: 1510
  helix:  0.64 (0.27), residues: 349
  sheet: -1.55 (0.25), residues: 391
  loop : -2.94 (0.20), residues: 770

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 166 
 TYR   0.028   0.002   TYR C  41 
 PHE   0.022   0.002   PHE A 738 
 TRP   0.017   0.002   TRP A 206 
 HIS   0.005   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00525 (12124)
  covalent geometry    : angle       0.77300 (16483)
  SS BOND              : bond        0.00398 (    1)
  SS BOND              : angle       0.84959 (    2)
  hydrogen bonds       : bond        0.04511 (  522)
  hydrogen bonds       : angle       6.11819 ( 1440)

*********************** 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: 44
    poor density    : 200
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8420 (tp40) cc_final: 0.8210 (tp40)
REVERT: A  450 LEU cc_start: 0.5437 (OUTLIER) cc_final: 0.5038 (mp)
REVERT: A  546 TRP cc_start: 0.7859 (OUTLIER) cc_final: 0.7643 (m-90)
REVERT: A  549 LEU cc_start: 0.8402 (mm) cc_final: 0.8038 (mm)
REVERT: A  641 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6687 (pp)
REVERT: A  777 MET cc_start: 0.7134 (ptm) cc_final: 0.6071 (tpt)
REVERT: B  215 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7495 (tpt90)
REVERT: B  306 MET cc_start: 0.6998 (tmm) cc_final: 0.6531 (tmm)
REVERT: B  308 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6650 (mt)
REVERT: C   43 GLU cc_start: 0.8542 (mp0) cc_final: 0.7974 (mp0)
REVERT: C   73 SER cc_start: 0.8038 (p) cc_final: 0.7802 (p)
REVERT: D   84 ASP cc_start: 0.8372 (m-30) cc_final: 0.7983 (p0)
REVERT: D  111 MET cc_start: 0.9260 (mmm) cc_final: 0.9011 (tpp)
REVERT: E   66 ASP cc_start: 0.8294 (t0) cc_final: 0.7872 (t0)
  outliers start: 44
  outliers final: 28
  residues processed: 232
  average time/residue: 0.0982
  time to fit residues: 34.1279
Evaluate side-chains
  222 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 190
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 VAL
Chi-restraints excluded: chain A residue  129 THR
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  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  546 TRP
Chi-restraints excluded: chain A residue  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  665 SER
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  352 GLU
Chi-restraints excluded: chain B residue  369 THR
Chi-restraints excluded: chain D residue   54 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 105 optimal weight:    8.9990
   chunk 117 optimal weight:    9.9990
   chunk 131 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 40 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 143 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
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**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 302 ASN
** 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 = 0.4147 r_free = 0.4147 target = 0.181945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.150110 restraints weight = 18122.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.148159 restraints weight = 21681.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.149988 restraints weight = 21037.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.150303 restraints weight = 14782.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.150615 restraints weight = 14820.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.2276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12125  Z= 0.175
  Angle     :  0.719  10.269  16485  Z= 0.382
  Chirality :  0.047   0.225   1800
  Planarity :  0.005   0.054   2175
  Dihedral  :  6.571  40.965   1669
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 13.52
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 11.66 %
    Favored  : 88.21 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.91 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.20), residues: 1510
  helix:  0.77 (0.27), residues: 349
  sheet: -1.51 (0.25), residues: 387
  loop : -2.90 (0.20), residues: 774

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 421 
 TYR   0.019   0.002   TYR C  41 
 PHE   0.016   0.001   PHE A 738 
 TRP   0.016   0.002   TRP B 279 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (12124)
  covalent geometry    : angle       0.71912 (16483)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       0.47291 (    2)
  hydrogen bonds       : bond        0.04211 (  522)
  hydrogen bonds       : angle       5.95695 ( 1440)

*********************** 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
  235 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 200
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8335 (tp40) cc_final: 0.8116 (tp40)
REVERT: A  262 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7805 (mm-30)
REVERT: A  450 LEU cc_start: 0.5581 (OUTLIER) cc_final: 0.5104 (mp)
REVERT: A  549 LEU cc_start: 0.8348 (mm) cc_final: 0.7989 (mm)
REVERT: A  641 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6646 (pp)
REVERT: A  777 MET cc_start: 0.6905 (ptm) cc_final: 0.6123 (tpt)
REVERT: B  215 ARG cc_start: 0.7772 (mmm160) cc_final: 0.7467 (tpt90)
REVERT: B  306 MET cc_start: 0.6921 (tmm) cc_final: 0.6466 (tmm)
REVERT: B  308 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6582 (mt)
REVERT: C   73 SER cc_start: 0.7975 (p) cc_final: 0.7728 (p)
REVERT: D   84 ASP cc_start: 0.8313 (m-30) cc_final: 0.7834 (p0)
REVERT: D  111 MET cc_start: 0.9225 (mmm) cc_final: 0.8916 (tpp)
REVERT: E   66 ASP cc_start: 0.8158 (t0) cc_final: 0.7798 (t0)
  outliers start: 35
  outliers final: 26
  residues processed: 226
  average time/residue: 0.0964
  time to fit residues: 32.7484
Evaluate side-chains
  219 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 190
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
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  194 ILE
Chi-restraints excluded: chain A residue  240 ILE
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  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  166 THR
Chi-restraints excluded: chain B residue  222 GLU
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 136 optimal weight:    0.5980
   chunk 120 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 91 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 84 optimal weight:    0.0970
   chunk 70 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   chunk 89 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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**
** E  83 HIS ** 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 = 0.4194 r_free = 0.4194 target = 0.186509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.155934 restraints weight = 18125.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.155495 restraints weight = 22893.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157047 restraints weight = 19918.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.157150 restraints weight = 13430.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.157929 restraints weight = 13534.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2707

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= 0.130
  Angle     :  0.695   8.952  16485  Z= 0.364
  Chirality :  0.046   0.197   1800
  Planarity :  0.005   0.049   2175
  Dihedral  :  6.149  38.295   1669
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.60 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.38 %
    Favored  : 79.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.20), residues: 1510
  helix:  0.93 (0.27), residues: 349
  sheet: -1.42 (0.25), residues: 388
  loop : -2.85 (0.20), residues: 773

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 421 
 TYR   0.022   0.001   TYR D 184 
 PHE   0.024   0.001   PHE D  64 
 TRP   0.061   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12124)
  covalent geometry    : angle       0.69523 (16483)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.24108 (    2)
  hydrogen bonds       : bond        0.03920 (  522)
  hydrogen bonds       : angle       5.72243 ( 1440)

*********************** 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
  240 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 209
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8184 (tp40) cc_final: 0.7935 (tp40)
REVERT: A  368 GLU cc_start: 0.7108 (tp30) cc_final: 0.6398 (tp30)
REVERT: A  421 ARG cc_start: 0.6196 (tmm160) cc_final: 0.5807 (ptt-90)
REVERT: A  450 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4827 (mt)
REVERT: A  549 LEU cc_start: 0.8191 (mm) cc_final: 0.7861 (mm)
REVERT: A  641 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6515 (pp)
REVERT: A  777 MET cc_start: 0.6627 (ptm) cc_final: 0.5845 (tpt)
REVERT: B  215 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7473 (tpt90)
REVERT: B  306 MET cc_start: 0.6582 (tmm) cc_final: 0.6239 (tmm)
REVERT: B  308 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6578 (mt)
REVERT: C   43 GLU cc_start: 0.8394 (mp0) cc_final: 0.7680 (mp0)
REVERT: C   73 SER cc_start: 0.7854 (p) cc_final: 0.7642 (p)
REVERT: D   84 ASP cc_start: 0.8234 (m-30) cc_final: 0.7754 (p0)
REVERT: D  111 MET cc_start: 0.9149 (mmm) cc_final: 0.8809 (tpp)
REVERT: D  223 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8551 (ttm-80)
REVERT: E   66 ASP cc_start: 0.7977 (t0) cc_final: 0.7599 (t0)
  outliers start: 31
  outliers final: 22
  residues processed: 231
  average time/residue: 0.1035
  time to fit residues: 35.5712
Evaluate side-chains
  216 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 191
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
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  308 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  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   91 GLU
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  254 VAL
Chi-restraints excluded: chain B residue  263 TYR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain D residue   54 GLN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 114 optimal weight:    7.9990
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   chunk 67 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 138 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 466 GLN
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 359 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.174329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.141569 restraints weight = 18552.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139182 restraints weight = 25023.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.140935 restraints weight = 23848.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.142900 restraints weight = 15668.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.142991 restraints weight = 13895.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.072  12125  Z= 0.397
  Angle     :  0.884  10.556  16485  Z= 0.474
  Chirality :  0.052   0.278   1800
  Planarity :  0.007   0.068   2175
  Dihedral  :  7.035  42.558   1669
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 13.84 %
    Favored  : 86.09 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.07 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.41 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.51 (0.20), residues: 1510
  helix:  0.68 (0.27), residues: 345
  sheet: -1.61 (0.24), residues: 400
  loop : -2.91 (0.20), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 166 
 TYR   0.024   0.003   TYR B 263 
 PHE   0.031   0.003   PHE A 169 
 TRP   0.022   0.003   TRP A 376 
 HIS   0.008   0.002   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00888 (12124)
  covalent geometry    : angle       0.88356 (16483)
  SS BOND              : bond        0.00463 (    1)
  SS BOND              : angle       1.20914 (    2)
  hydrogen bonds       : bond        0.04985 (  522)
  hydrogen bonds       : angle       6.28250 ( 1440)

*********************** 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
  246 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 194
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8415 (tp40) cc_final: 0.8190 (tp40)
REVERT: A  372 MET cc_start: 0.7852 (mtm) cc_final: 0.7572 (mtm)
REVERT: A  450 LEU cc_start: 0.5561 (OUTLIER) cc_final: 0.5161 (mt)
REVERT: A  549 LEU cc_start: 0.8416 (mm) cc_final: 0.8075 (mm)
REVERT: A  641 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6806 (pp)
REVERT: A  719 ILE cc_start: 0.8099 (mp) cc_final: 0.7749 (mt)
REVERT: A  777 MET cc_start: 0.7052 (ptm) cc_final: 0.6208 (tpt)
REVERT: A  789 GLN cc_start: 0.8270 (tp40) cc_final: 0.7453 (pt0)
REVERT: C   73 SER cc_start: 0.8115 (p) cc_final: 0.7869 (p)
REVERT: D   84 ASP cc_start: 0.8514 (m-30) cc_final: 0.7925 (p0)
REVERT: D  111 MET cc_start: 0.9323 (mmm) cc_final: 0.9020 (tpp)
REVERT: E   66 ASP cc_start: 0.8388 (t0) cc_final: 0.8011 (t0)
  outliers start: 52
  outliers final: 40
  residues processed: 232
  average time/residue: 0.0969
  time to fit residues: 33.7396
Evaluate side-chains
  229 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 187
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
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  194 ILE
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  392 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  513 VAL
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  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  228 TRP
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  303 ASP
Chi-restraints excluded: chain B residue  305 VAL
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  362 VAL
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   54 GLN
Chi-restraints excluded: chain D residue   71 VAL
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   93 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 122 optimal weight:    3.9990
   chunk 0 optimal weight:   30.0000
   chunk 148 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 135 optimal weight:    0.6980
   chunk 123 optimal weight:    5.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 334 ASN
** 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 = 0.4161 r_free = 0.4161 target = 0.183029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.151502 restraints weight = 18131.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.150307 restraints weight = 21979.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.151773 restraints weight = 21846.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152449 restraints weight = 14713.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.152722 restraints weight = 13487.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12125  Z= 0.155
  Angle     :  0.733  10.507  16485  Z= 0.386
  Chirality :  0.047   0.222   1800
  Planarity :  0.005   0.047   2175
  Dihedral  :  6.385  39.615   1669
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.79 %
    Favored  : 89.14 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.64 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.43 (0.20), residues: 1510
  helix:  0.78 (0.27), residues: 348
  sheet: -1.58 (0.25), residues: 390
  loop : -2.87 (0.20), residues: 772

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 166 
 TYR   0.023   0.002   TYR B 333 
 PHE   0.025   0.001   PHE A 738 
 TRP   0.024   0.002   TRP A 546 
 HIS   0.003   0.001   HIS B 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12124)
  covalent geometry    : angle       0.73352 (16483)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       0.51112 (    2)
  hydrogen bonds       : bond        0.04147 (  522)
  hydrogen bonds       : angle       5.89091 ( 1440)

*********************** 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
  231 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 196
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  217 GLN cc_start: 0.8283 (tp40) cc_final: 0.8046 (tp40)
REVERT: A  450 LEU cc_start: 0.5279 (OUTLIER) cc_final: 0.4934 (mt)
REVERT: A  549 LEU cc_start: 0.8229 (mm) cc_final: 0.7856 (mm)
REVERT: A  641 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6591 (pp)
REVERT: A  719 ILE cc_start: 0.8048 (mp) cc_final: 0.7638 (mt)
REVERT: A  777 MET cc_start: 0.6728 (ptm) cc_final: 0.5856 (tpt)
REVERT: A  789 GLN cc_start: 0.8154 (tp40) cc_final: 0.7433 (pt0)
REVERT: B  306 MET cc_start: 0.6923 (tmm) cc_final: 0.6297 (tmm)
REVERT: C   43 GLU cc_start: 0.8122 (mp0) cc_final: 0.7870 (mp0)
REVERT: C   73 SER cc_start: 0.8006 (p) cc_final: 0.7771 (p)
REVERT: D   84 ASP cc_start: 0.8391 (m-30) cc_final: 0.7772 (p0)
REVERT: D   99 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.7918 (p0)
REVERT: D  111 MET cc_start: 0.9234 (mmm) cc_final: 0.8904 (tpp)
REVERT: E   66 ASP cc_start: 0.8082 (t0) cc_final: 0.7804 (t0)
  outliers start: 35
  outliers final: 23
  residues processed: 223
  average time/residue: 0.0973
  time to fit residues: 32.1110
Evaluate side-chains
  209 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 183
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  194 ILE
Chi-restraints excluded: chain A residue  240 ILE
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  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  254 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain D residue   54 GLN
Chi-restraints excluded: chain D residue   76 ILE
Chi-restraints excluded: chain D residue   99 ASN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain D residue  215 LEU
Chi-restraints excluded: chain E residue   68 PHE
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 146 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   chunk 84 optimal weight:    8.9990
   chunk 78 optimal weight:    0.0270
   chunk 141 optimal weight:    0.9990
   chunk 10 optimal weight:    8.9990
   chunk 76 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 138 optimal weight:    0.9980
   overall best weight:    0.7442

-------------------------------------------------------------------------------
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 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 HIS ** 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 = 0.4183 r_free = 0.4183 target = 0.185102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.154102 restraints weight = 18009.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.154188 restraints weight = 23284.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.155831 restraints weight = 19490.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.155488 restraints weight = 14986.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.157582 restraints weight = 13173.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12125  Z= 0.140
  Angle     :  0.713  10.880  16485  Z= 0.374
  Chirality :  0.046   0.233   1800
  Planarity :  0.005   0.048   2175
  Dihedral  :  6.113  37.920   1669
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.93 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 19.87 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.21), residues: 1510
  helix:  0.91 (0.27), residues: 346
  sheet: -1.53 (0.25), residues: 399
  loop : -2.77 (0.20), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 223 
 TYR   0.031   0.001   TYR B 333 
 PHE   0.024   0.001   PHE A 738 
 TRP   0.025   0.002   TRP A 546 
 HIS   0.005   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12124)
  covalent geometry    : angle       0.71298 (16483)
  SS BOND              : bond        0.00180 (    1)
  SS BOND              : angle       0.23735 (    2)
  hydrogen bonds       : bond        0.03929 (  522)
  hydrogen bonds       : angle       5.72063 ( 1440)

*********************** 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
  221 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 188
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.3854 (OUTLIER) cc_final: 0.3222 (pmm)
REVERT: A  217 GLN cc_start: 0.8230 (tp40) cc_final: 0.7991 (tp40)
REVERT: A  450 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5217 (mt)
REVERT: A  549 LEU cc_start: 0.8170 (mm) cc_final: 0.7780 (mm)
REVERT: A  641 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6475 (pp)
REVERT: A  719 ILE cc_start: 0.8069 (mp) cc_final: 0.7659 (mt)
REVERT: A  777 MET cc_start: 0.6416 (ptm) cc_final: 0.5604 (tpt)
REVERT: A  789 GLN cc_start: 0.8109 (tp40) cc_final: 0.7245 (pt0)
REVERT: B   32 MET cc_start: 0.8193 (mpp) cc_final: 0.7579 (mtm)
REVERT: B   48 TRP cc_start: 0.6761 (OUTLIER) cc_final: 0.6119 (t60)
REVERT: B  348 TRP cc_start: 0.7335 (m-10) cc_final: 0.6821 (m-10)
REVERT: C   43 GLU cc_start: 0.8073 (mp0) cc_final: 0.7869 (mp0)
REVERT: C   73 SER cc_start: 0.7889 (p) cc_final: 0.7636 (p)
REVERT: C   80 LEU cc_start: 0.8305 (pt) cc_final: 0.8059 (pp)
REVERT: D   84 ASP cc_start: 0.8325 (m-30) cc_final: 0.7711 (p0)
REVERT: D   99 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7919 (p0)
REVERT: E   66 ASP cc_start: 0.7920 (t0) cc_final: 0.7563 (t0)
  outliers start: 33
  outliers final: 22
  residues processed: 211
  average time/residue: 0.0974
  time to fit residues: 30.5018
Evaluate side-chains
  213 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 186
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
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  194 ILE
Chi-restraints excluded: chain A residue  240 ILE
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  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   91 GLU
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  254 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain D residue   54 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 137 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 93 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 145 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0470
   overall best weight:    0.7682

-------------------------------------------------------------------------------
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**
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 HIS ** 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 = 0.186858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.155945 restraints weight = 18217.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.155121 restraints weight = 23360.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.156798 restraints weight = 21305.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.156235 restraints weight = 14665.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.156970 restraints weight = 14044.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12125  Z= 0.134
  Angle     :  0.704  10.036  16485  Z= 0.366
  Chirality :  0.045   0.165   1800
  Planarity :  0.005   0.053   2175
  Dihedral  :  5.905  36.677   1669
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 10.53 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 19.80 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.21), residues: 1510
  helix:  1.04 (0.27), residues: 347
  sheet: -1.42 (0.25), residues: 399
  loop : -2.67 (0.21), residues: 764

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 392 
 TYR   0.041   0.001   TYR B 333 
 PHE   0.021   0.001   PHE D  64 
 TRP   0.039   0.002   TRP A 546 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (12124)
  covalent geometry    : angle       0.70387 (16483)
  SS BOND              : bond        0.00184 (    1)
  SS BOND              : angle       0.26442 (    2)
  hydrogen bonds       : bond        0.03823 (  522)
  hydrogen bonds       : angle       5.60268 ( 1440)

********************** 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
  226 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 195
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 MET cc_start: 0.3836 (OUTLIER) cc_final: 0.3199 (pmm)
REVERT: A  217 GLN cc_start: 0.8225 (tp40) cc_final: 0.7983 (tp40)
REVERT: A  261 THR cc_start: 0.8228 (t) cc_final: 0.7928 (p)
REVERT: A  450 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5172 (mt)
REVERT: A  549 LEU cc_start: 0.8261 (mm) cc_final: 0.7878 (mm)
REVERT: A  619 VAL cc_start: 0.7995 (t) cc_final: 0.7612 (m)
REVERT: A  641 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6537 (pp)
REVERT: A  719 ILE cc_start: 0.8028 (mp) cc_final: 0.7583 (mt)
REVERT: A  741 MET cc_start: 0.8441 (ptm) cc_final: 0.8082 (ptt)
REVERT: A  769 SER cc_start: 0.7646 (m) cc_final: 0.7204 (t)
REVERT: A  777 MET cc_start: 0.6212 (ptm) cc_final: 0.5422 (tpt)
REVERT: A  789 GLN cc_start: 0.8064 (tp40) cc_final: 0.7787 (mm110)
REVERT: B   32 MET cc_start: 0.8159 (mpp) cc_final: 0.7549 (mtm)
REVERT: C   73 SER cc_start: 0.7819 (p) cc_final: 0.7576 (p)
REVERT: C   80 LEU cc_start: 0.8325 (pt) cc_final: 0.8075 (pp)
REVERT: D   84 ASP cc_start: 0.8288 (m-30) cc_final: 0.7698 (p0)
REVERT: E   66 ASP cc_start: 0.7964 (t0) cc_final: 0.7659 (t0)
  outliers start: 31
  outliers final: 24
  residues processed: 212
  average time/residue: 0.0945
  time to fit residues: 29.8939
Evaluate side-chains
  210 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 183
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 MET
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  194 ILE
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  560 ASP
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain B residue   35 LEU
Chi-restraints excluded: chain B residue   91 GLU
Chi-restraints excluded: chain B residue  153 SER
Chi-restraints excluded: chain B residue  166 THR
Chi-restraints excluded: chain B residue  189 MET
Chi-restraints excluded: chain B residue  254 VAL
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain D residue   54 GLN
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 72 optimal weight:    5.9990
   chunk 101 optimal weight:    0.3980
   chunk 99 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 36 optimal weight:    0.0050
   chunk 124 optimal weight:    3.9990
   chunk 128 optimal weight:    0.9980
   chunk 119 optimal weight:    7.9990
   chunk 76 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.0798

-------------------------------------------------------------------------------
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 223 GLN
B 225 GLN
B 334 ASN
D  99 ASN
** D 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.186259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.154366 restraints weight = 18198.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.154004 restraints weight = 22652.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.155747 restraints weight = 19574.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.156024 restraints weight = 12717.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.156151 restraints weight = 13869.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3505

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= 0.145
  Angle     :  0.705   8.913  16485  Z= 0.369
  Chirality :  0.045   0.168   1800
  Planarity :  0.005   0.056   2175
  Dihedral  :  5.899  37.508   1669
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 11.19 %
    Favored  : 88.74 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 20.11 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.34 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.01 (0.21), residues: 1510
  helix:  1.15 (0.27), residues: 347
  sheet: -1.31 (0.25), residues: 398
  loop : -2.63 (0.21), residues: 765

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 166 
 TYR   0.040   0.001   TYR B 333 
 PHE   0.019   0.001   PHE A 738 
 TRP   0.036   0.002   TRP A 546 
 HIS   0.003   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12124)
  covalent geometry    : angle       0.70531 (16483)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       0.27368 (    2)
  hydrogen bonds       : bond        0.03850 (  522)
  hydrogen bonds       : angle       5.55654 ( 1440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1685.34 seconds
wall clock time: 30 minutes 10.08 seconds (1810.08 seconds total)