Starting phenix.real_space_refine
on Fri Aug 22 19:21:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8efd_28080/08_2025/8efd_28080.map"
  }
  resolution = 3.8
  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=   0.001
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      40      5.16       5
     C    4524      2.51       5
     N    1210      2.21       5
     O    1333      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7107
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5967
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 5967
          Classifications: {'peptide': 740}
          Link IDs: {'PTRANS': 28, 'TRANS': 711}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 1140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 1140
          Classifications: {'peptide': 146}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 142}
  Time building chain proxies: 1.80, per 1000 atoms: 0.25
  Number of scatterers: 7107
  At special positions: 0
  Unit cell: (86.24, 127.204, 117.502, 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      40     16.00
     O    1333      8.00
     N    1210      7.00
     C    4524      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 373.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1658

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 9 sheets defined
      57.2% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 11
      removed outlier: 6.202A  pdb=" N   ALA A  11 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 17
      removed outlier: 3.524A  pdb=" N   LEU A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.759A  pdb=" N   THR A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 97 through 111
      removed outlier: 3.675A  pdb=" N   LEU A 102 " --> pdb=" O   GLU A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 134
      removed outlier: 4.436A  pdb=" N   TYR A 134 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 131 through 134'
    Processing helix  chain 'A' and resid 135 through 143
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 183 through 197
    Processing helix  chain 'A' and resid 217 through 231
      Proline residue:  A 225  - end of helix
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 283 through 290
      removed outlier: 4.434A  pdb=" N   TYR A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 302
    Processing helix  chain 'A' and resid 306 through 309
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 324 through 338
    Processing helix  chain 'A' and resid 343 through 359
      removed outlier: 3.577A  pdb=" N   ASN A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 416 through 448
    Processing helix  chain 'A' and resid 472 through 504
    Processing helix  chain 'A' and resid 513 through 526
      removed outlier: 3.709A  pdb=" N   LEU A 517 " --> pdb=" O   PHE A 513 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   ALA A 519 " --> pdb=" O   MET A 515 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   CYS A 520 " --> pdb=" O   ASP A 516 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 540
      removed outlier: 3.551A  pdb=" N   CYS A 538 " --> pdb=" O   LEU A 534 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   MET A 539 " --> pdb=" O   GLU A 535 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE A 540 " --> pdb=" O   GLU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
    Processing helix  chain 'A' and resid 592 through 598
      removed outlier: 3.971A  pdb=" N   LYS A 598 " --> pdb=" O   LEU A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 611
    Processing helix  chain 'A' and resid 615 through 620
    Processing helix  chain 'A' and resid 647 through 664
      removed outlier: 3.913A  pdb=" N   SER A 664 " --> pdb=" O   THR A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 685 through 696
    Processing helix  chain 'A' and resid 697 through 707
    Processing helix  chain 'A' and resid 715 through 723
      removed outlier: 3.506A  pdb=" N   ARG A 723 " --> pdb=" O   ARG A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 749
    Processing helix  chain 'A' and resid 752 through 754
      No H-bonds generated for 'chain 'A' and resid 752 through 754'
    Processing helix  chain 'A' and resid 766 through 796
      removed outlier: 3.915A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 766 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   GLY A 771 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 57
    Processing helix  chain 'B' and resid 65 through 75
      removed outlier: 3.962A  pdb=" N   VAL B  69 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 89
    Processing helix  chain 'B' and resid 95 through 100
    Processing helix  chain 'B' and resid 103 through 116
      Proline residue:  B 109  - end of helix
      removed outlier: 3.655A  pdb=" N   ASN B 116 " --> pdb=" O   GLN B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.547A  pdb=" N   VAL B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 153
    Processing helix  chain 'B' and resid 158 through 166
    Processing helix  chain 'B' and resid 178 through 188
    Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 118
      removed outlier: 4.053A  pdb=" N   PHE A 121 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 266
      removed outlier: 6.691A  pdb=" N   LYS A 246 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   LEU A 460 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   ILE A 248 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   GLY A 458 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE A 250 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   PHE A 456 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLN A 172 " --> pdb=" O   PHE A 456 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 233
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA6, first strand: chain 'A' and resid 403 through 406
    Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 581
      removed outlier: 3.726A  pdb=" N   PHE A 577 " --> pdb=" O   TYR A 588 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 711 through 714
    Processing sheet with id=AA9, first strand: chain 'B' and resid 140 through 142
      removed outlier: 3.630A  pdb=" N   VAL B 141 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1032 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.79

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2344
        1.34 -     1.46: 1365
        1.46 -     1.58: 3466
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 7245
  Sorted by residual:
  bond pdb=" CG  GLU A 775 "
       pdb=" CD  GLU A 775 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.11e+00
  bond pdb=" C   GLU A 374 "
       pdb=" O   GLU A 374 "
    ideal  model  delta    sigma   weight residual
    1.245  1.229  0.016 1.53e-02 4.27e+03 1.08e+00
  bond pdb=" CG1 ILE A 289 "
       pdb=" CD1 ILE A 289 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.80e-01
  bond pdb=" N   LYS A 570 "
       pdb=" CA  LYS A 570 "
    ideal  model  delta    sigma   weight residual
    1.457  1.469 -0.011 1.29e-02 6.01e+03 7.48e-01
  bond pdb=" C   GLU A 374 "
       pdb=" N   PRO A 375 "
    ideal  model  delta    sigma   weight residual
    1.330  1.339 -0.009 1.22e-02 6.72e+03 5.83e-01
  ... (remaining 7240 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 9335
        1.03 -     2.06: 330
        2.06 -     3.09: 57
        3.09 -     4.11: 27
        4.11 -     5.14: 5
  Bond angle restraints: 9754
  Sorted by residual:
  angle pdb=" N   GLU A 775 "
        pdb=" CA  GLU A 775 "
        pdb=" CB  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     110.28  115.42   -5.14 1.55e+00 4.16e-01 1.10e+01
  angle pdb=" C   GLU A 774 "
        pdb=" N   GLU A 775 "
        pdb=" CA  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     120.31  115.74    4.57 1.52e+00 4.33e-01 9.04e+00
  angle pdb=" CA  GLU A 775 "
        pdb=" CB  GLU A 775 "
        pdb=" CG  GLU A 775 "
      ideal   model   delta    sigma   weight residual
     114.10  118.94   -4.84 2.00e+00 2.50e-01 5.85e+00
  angle pdb=" CA  PRO A 375 "
        pdb=" C   PRO A 375 "
        pdb=" O   PRO A 375 "
      ideal   model   delta    sigma   weight residual
     122.08  119.30    2.78 1.28e+00 6.10e-01 4.73e+00
  angle pdb=" N   PHE A 364 "
        pdb=" CA  PHE A 364 "
        pdb=" C   PHE A 364 "
      ideal   model   delta    sigma   weight residual
     110.91  113.33   -2.42 1.17e+00 7.31e-01 4.26e+00
  ... (remaining 9749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3959
       17.91 -    35.81: 365
       35.81 -    53.72: 61
       53.72 -    71.63: 6
       71.63 -    89.53: 9
  Dihedral angle restraints: 4400
    sinusoidal: 1829
      harmonic: 2571
  Sorted by residual:
  dihedral pdb=" CB  GLU A 328 "
           pdb=" CG  GLU A 328 "
           pdb=" CD  GLU A 328 "
           pdb=" OE1 GLU A 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.53   89.53     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A  98 "
           pdb=" CG  GLU A  98 "
           pdb=" CD  GLU A  98 "
           pdb=" OE1 GLU A  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.09   88.09     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CA  ARG A 706 "
           pdb=" CB  ARG A 706 "
           pdb=" CG  ARG A 706 "
           pdb=" CD  ARG A 706 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.94   50.94     3      1.50e+01 4.44e-03 8.96e+00
  ... (remaining 4397 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 682
       0.027 -    0.055: 248
       0.055 -    0.082: 75
       0.082 -    0.109: 38
       0.109 -    0.136: 17
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" CA  VAL A 459 "
            pdb=" N   VAL A 459 "
            pdb=" C   VAL A 459 "
            pdb=" CB  VAL A 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.64e-01
  chirality pdb=" CA  ILE A 674 "
            pdb=" N   ILE A 674 "
            pdb=" C   ILE A 674 "
            pdb=" CB  ILE A 674 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  PRO A 710 "
            pdb=" N   PRO A 710 "
            pdb=" C   PRO A 710 "
            pdb=" CB  PRO A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1057 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 224 "   -0.016 5.00e-02 4.00e+02   2.46e-02 9.65e-01
        pdb=" N   PRO A 225 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 225 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 225 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 609 "    0.006 2.00e-02 2.50e+03   6.55e-03 8.57e-01
        pdb=" CG  TYR A 609 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 609 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 609 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 609 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 609 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 609 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 609 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 709 "    0.015 5.00e-02 4.00e+02   2.22e-02 7.85e-01
        pdb=" N   PRO A 710 "   -0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO A 710 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO A 710 "    0.012 5.00e-02 4.00e+02
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 117
        2.62 -     3.19: 6966
        3.19 -     3.76: 11311
        3.76 -     4.33: 14687
        4.33 -     4.90: 24028
  Nonbonded interactions: 57109
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 235 "
            pdb=" O   ASN A 238 "
     model   vdw
     2.048 3.040
  nonbonded pdb=" O   THR A 449 "
            pdb=" NH2 ARG A 453 "
     model   vdw
     2.086 3.120
  nonbonded pdb=" O   ALA A 141 "
            pdb=" NZ  LYS A 145 "
     model   vdw
     2.092 3.120
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   ALA A 767 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" O   LEU A 166 "
            pdb=" NH1 ARG A 169 "
     model   vdw
     2.119 3.120
  ... (remaining 57104 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:             8.400
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     7.990
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
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      :  0.002   0.039   7245  Z= 0.107
  Angle     :  0.492   5.144   9754  Z= 0.272
  Chirality :  0.037   0.136   1060
  Planarity :  0.002   0.025   1269
  Dihedral  : 14.097  89.535   2742
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.39 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.29), residues: 876
  helix:  1.91 (0.25), residues: 446
  sheet: -1.37 (0.62), residues: 82
  loop : -0.78 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.016   0.001   TYR A 609 
 PHE   0.013   0.001   PHE A 510 
 TRP   0.003   0.001   TRP A 130 
 HIS   0.006   0.001   HIS B 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 7245)
  covalent geometry    : angle       0.49222 ( 9754)
  hydrogen bonds       : bond        0.14225 (  356)
  hydrogen bonds       : angle       6.02469 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  165 MET cc_start: 0.8946 (tmm) cc_final: 0.8712 (tmm)
REVERT: A  388 MET cc_start: 0.8990 (mpp) cc_final: 0.8761 (mpp)
REVERT: A  439 MET cc_start: 0.9109 (mpp) cc_final: 0.8881 (mpp)
REVERT: A  546 MET cc_start: 0.8837 (tpt) cc_final: 0.8613 (tpp)
REVERT: A  776 MET cc_start: 0.9460 (mmp) cc_final: 0.9223 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0663
  time to fit residues: 5.9005
Evaluate side-chains
  45 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 163 GLN
A 691 HIS
A 711 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.049172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.039366 restraints weight = 61857.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.040324 restraints weight = 32874.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.040968 restraints weight = 20921.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.041387 restraints weight = 14987.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.041624 restraints weight = 11865.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7245  Z= 0.199
  Angle     :  0.622   6.418   9754  Z= 0.328
  Chirality :  0.042   0.158   1060
  Planarity :  0.004   0.048   1269
  Dihedral  :  4.267  16.617    954
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  8.84 %
    Favored  : 89.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.29), residues: 876
  helix:  1.46 (0.24), residues: 456
  sheet: -1.49 (0.60), residues: 82
  loop : -0.97 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 453 
 TYR   0.017   0.002   TYR A 609 
 PHE   0.026   0.002   PHE B 181 
 TRP   0.008   0.001   TRP A 593 
 HIS   0.005   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7245)
  covalent geometry    : angle       0.62176 ( 9754)
  hydrogen bonds       : bond        0.03764 (  356)
  hydrogen bonds       : angle       5.14105 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.6985 (ttm) cc_final: 0.6505 (ttm)
REVERT: A  546 MET cc_start: 0.8617 (tpt) cc_final: 0.8289 (tpp)
REVERT: B   97 MET cc_start: 0.4825 (ptt) cc_final: 0.3822 (tpt)
  outliers start: 9
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0832
  time to fit residues: 6.6326
Evaluate side-chains
  51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASN
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.049716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.039736 restraints weight = 61694.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.040697 restraints weight = 33256.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.041350 restraints weight = 21347.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.041782 restraints weight = 15366.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.041978 restraints weight = 12152.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7245  Z= 0.120
  Angle     :  0.537   5.735   9754  Z= 0.282
  Chirality :  0.040   0.133   1060
  Planarity :  0.003   0.034   1269
  Dihedral  :  4.047  15.790    954
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.92 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.29), residues: 876
  helix:  1.39 (0.24), residues: 461
  sheet: -1.42 (0.60), residues: 82
  loop : -0.90 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 131 
 TYR   0.050   0.002   TYR A 609 
 PHE   0.009   0.001   PHE A 669 
 TRP   0.004   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7245)
  covalent geometry    : angle       0.53672 ( 9754)
  hydrogen bonds       : bond        0.03412 (  356)
  hydrogen bonds       : angle       4.87420 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.6916 (ttm) cc_final: 0.6435 (ttm)
REVERT: A  195 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7989 (m-80)
REVERT: A  546 MET cc_start: 0.8548 (tpt) cc_final: 0.8282 (tpp)
REVERT: B   97 MET cc_start: 0.4885 (ptt) cc_final: 0.4010 (tpt)
  outliers start: 10
  outliers final: 5
  residues processed: 52
  average time/residue: 0.0618
  time to fit residues: 4.9843
Evaluate side-chains
  51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0570
   chunk 86 optimal weight:    5.9990
   chunk 50 optimal weight:    0.2980
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   overall best weight:    0.2696

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN
A 171 ASN
B 120 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.050173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.040168 restraints weight = 61222.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.041165 restraints weight = 33383.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.041812 restraints weight = 21373.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.042255 restraints weight = 15431.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.042512 restraints weight = 12215.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7245  Z= 0.102
  Angle     :  0.530   7.051   9754  Z= 0.274
  Chirality :  0.039   0.151   1060
  Planarity :  0.003   0.032   1269
  Dihedral  :  3.909  20.074    954
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.00 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.29), residues: 876
  helix:  1.49 (0.25), residues: 456
  sheet: -1.37 (0.61), residues: 82
  loop : -0.79 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 777 
 TYR   0.011   0.001   TYR A 162 
 PHE   0.022   0.001   PHE B 181 
 TRP   0.003   0.001   TRP A 508 
 HIS   0.001   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 7245)
  covalent geometry    : angle       0.53015 ( 9754)
  hydrogen bonds       : bond        0.03046 (  356)
  hydrogen bonds       : angle       4.71734 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.6693 (ttm) cc_final: 0.6238 (ttm)
REVERT: A  195 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7872 (m-80)
REVERT: A  546 MET cc_start: 0.8548 (tpt) cc_final: 0.8293 (tpp)
REVERT: B   97 MET cc_start: 0.5414 (ptt) cc_final: 0.4652 (tpt)
  outliers start: 11
  outliers final: 5
  residues processed: 55
  average time/residue: 0.0687
  time to fit residues: 5.8007
Evaluate side-chains
  50 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  352 LEU
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 86 optimal weight:    0.2980
   chunk 39 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 26 optimal weight:    0.2980
   overall best weight:    0.3558

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.050058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.040062 restraints weight = 61531.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.041062 restraints weight = 33271.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.041677 restraints weight = 21267.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.042113 restraints weight = 15345.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.042387 restraints weight = 12213.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7245  Z= 0.100
  Angle     :  0.544   9.594   9754  Z= 0.275
  Chirality :  0.039   0.143   1060
  Planarity :  0.003   0.032   1269
  Dihedral  :  3.901  19.411    954
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 13.65 %
    Favored  : 85.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.29), residues: 876
  helix:  1.52 (0.25), residues: 457
  sheet: -1.37 (0.60), residues: 82
  loop : -0.77 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 453 
 TYR   0.012   0.001   TYR A 609 
 PHE   0.009   0.001   PHE B  53 
 TRP   0.009   0.001   TRP A 508 
 HIS   0.001   0.000   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7245)
  covalent geometry    : angle       0.54417 ( 9754)
  hydrogen bonds       : bond        0.02943 (  356)
  hydrogen bonds       : angle       4.61066 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7774 (m-80)
REVERT: A  546 MET cc_start: 0.8533 (tpt) cc_final: 0.8279 (tpp)
REVERT: B   97 MET cc_start: 0.5512 (ptt) cc_final: 0.4795 (tpt)
  outliers start: 10
  outliers final: 4
  residues processed: 50
  average time/residue: 0.0577
  time to fit residues: 4.4395
Evaluate side-chains
  49 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 14 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.049532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.039653 restraints weight = 60663.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.040613 restraints weight = 32177.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.041262 restraints weight = 20541.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.041678 restraints weight = 14702.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.041963 restraints weight = 11677.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.2539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7245  Z= 0.121
  Angle     :  0.562   7.943   9754  Z= 0.283
  Chirality :  0.039   0.144   1060
  Planarity :  0.003   0.032   1269
  Dihedral  :  3.911  18.484    954
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.95 %
    Favored  : 83.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.29), residues: 876
  helix:  1.49 (0.25), residues: 456
  sheet: -1.41 (0.60), residues: 82
  loop : -0.78 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 453 
 TYR   0.013   0.001   TYR A 609 
 PHE   0.021   0.001   PHE B 181 
 TRP   0.010   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 7245)
  covalent geometry    : angle       0.56156 ( 9754)
  hydrogen bonds       : bond        0.02955 (  356)
  hydrogen bonds       : angle       4.60907 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  113 MET cc_start: 0.6826 (ttm) cc_final: 0.6544 (ttm)
REVERT: A  163 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8917 (pm20)
REVERT: A  195 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7834 (m-80)
REVERT: A  546 MET cc_start: 0.8522 (tpt) cc_final: 0.8263 (tpp)
REVERT: B   97 MET cc_start: 0.5514 (ptt) cc_final: 0.4861 (tpt)
  outliers start: 14
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0718
  time to fit residues: 5.7846
Evaluate side-chains
  51 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0670
   chunk 78 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.049615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.039730 restraints weight = 60307.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.040732 restraints weight = 32416.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.041368 restraints weight = 20583.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.041796 restraints weight = 14773.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.042067 restraints weight = 11681.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7245  Z= 0.117
  Angle     :  0.566  10.698   9754  Z= 0.283
  Chirality :  0.039   0.141   1060
  Planarity :  0.003   0.031   1269
  Dihedral  :  3.912  19.817    954
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.60 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.29), residues: 876
  helix:  1.46 (0.25), residues: 461
  sheet: -1.40 (0.61), residues: 82
  loop : -0.79 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 453 
 TYR   0.013   0.001   TYR A 609 
 PHE   0.010   0.001   PHE A 230 
 TRP   0.008   0.001   TRP A 508 
 HIS   0.002   0.001   HIS A 491 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7245)
  covalent geometry    : angle       0.56632 ( 9754)
  hydrogen bonds       : bond        0.02905 (  356)
  hydrogen bonds       : angle       4.56741 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 45
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7767 (pmm) cc_final: 0.6876 (ptm)
REVERT: A  113 MET cc_start: 0.6955 (ttm) cc_final: 0.6690 (ttm)
REVERT: A  195 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7832 (m-80)
REVERT: A  546 MET cc_start: 0.8506 (tpt) cc_final: 0.8249 (tpp)
REVERT: B   97 MET cc_start: 0.5512 (ptt) cc_final: 0.4934 (tpt)
  outliers start: 16
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0577
  time to fit residues: 4.8925
Evaluate side-chains
  52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  271 SER
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  123 TYR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 76 optimal weight:    0.1980
   chunk 22 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0770
   chunk 72 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.2980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.2836

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

Flipped N/Q/H residues before XYZ refinement:
A 104 ASN
A 163 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.050107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.040061 restraints weight = 62027.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.041083 restraints weight = 33286.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.041710 restraints weight = 21166.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.042160 restraints weight = 15187.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.042415 restraints weight = 12026.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7245  Z= 0.097
  Angle     :  0.574  11.512   9754  Z= 0.281
  Chirality :  0.039   0.142   1060
  Planarity :  0.003   0.031   1269
  Dihedral  :  3.815  18.263    954
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.12 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.29), residues: 876
  helix:  1.51 (0.25), residues: 461
  sheet: -1.37 (0.61), residues: 82
  loop : -0.79 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 777 
 TYR   0.011   0.001   TYR A 164 
 PHE   0.024   0.001   PHE B 181 
 TRP   0.009   0.001   TRP A 508 
 HIS   0.001   0.000   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 7245)
  covalent geometry    : angle       0.57417 ( 9754)
  hydrogen bonds       : bond        0.02766 (  356)
  hydrogen bonds       : angle       4.46580 ( 1032)

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

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

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1752 Ramachandran restraints generated.
    876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 MET cc_start: 0.7810 (pmm) cc_final: 0.7057 (ptm)
REVERT: A  104 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7842 (t0)
REVERT: A  113 MET cc_start: 0.6780 (ttm) cc_final: 0.6543 (ttm)
REVERT: A  163 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8887 (pm20)
REVERT: A  195 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.7805 (m-80)
REVERT: A  546 MET cc_start: 0.8529 (tpt) cc_final: 0.8280 (tpp)
REVERT: B   97 MET cc_start: 0.5511 (ptt) cc_final: 0.4964 (tpt)
  outliers start: 12
  outliers final: 4
  residues processed: 53
  average time/residue: 0.0590
  time to fit residues: 4.7504
Evaluate side-chains
  52 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ASN
Chi-restraints excluded: chain A residue  163 GLN
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  678 THR
Chi-restraints excluded: chain B residue  148 HIS
Chi-restraints excluded: chain B residue  184 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run
    self.rsr_result = rsr_wrappers.run_real_space_refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__
    self._refined = macro_cycle_real_space.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs
    ro = mmtbx.refinement.real_space.individual_sites.easy(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__
    self.weight = mmtbx.refinement.real_space.weight.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine
    real_space_result = refinery(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine
    self.refined = maptbx.real_space_refinement_simple.lbfgs(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__
    O.minimizer = scitbx.lbfgs.run(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients
    gr_e = O.geometry_restraints_manager.energies_sites(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites
    pair_proxies = self.pair_proxies(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 66.3046 > 50:
  distance: 12 - 36:  29.455
  distance: 15 - 17:  21.432
  distance: 16 - 47:  27.956
  distance: 17 - 18:  27.181
  distance: 18 - 19:  14.183
  distance: 18 - 21:  30.902
  distance: 19 - 20:  40.412
  distance: 19 - 25:  40.012
  distance: 20 - 56:  22.598
  distance: 21 - 22:  17.790
  distance: 22 - 23:  34.441
  distance: 22 - 24:  22.352
  distance: 25 - 26:  28.544
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