Starting phenix.real_space_refine
on Thu Jul  2 12:20:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r8d_24316/07_2026/7r8d_24316.map"
  }
  resolution = 3.2
  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
-------------------------------------------------------------------------------
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=   0.005
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      68      5.16       5
     C    5756      2.51       5
     N    1414      2.21       5
     O    1524      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8762
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4269
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 545, 4269
          Classifications: {'peptide': 545}
          Link IDs: {'PTRANS': 18, 'TRANS': 526}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 112
          Unusual residues: {'CLR': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 112
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 112
          Unusual residues: {'CLR': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.68, per 1000 atoms: 0.19
  Number of scatterers: 8762
  At special positions: 0
  Unit cell: (102.459, 72.471, 120.785, 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      68     16.00
     O    1524      8.00
     N    1414      7.00
     C    5756      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 611 " - pdb=" SG  CYS A 617 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 611 " - pdb=" SG  CYS B 617 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 313.6 milliseconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2016

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 4 sheets defined
      60.9% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 131
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 173 through 186
    Processing helix  chain 'A' and resid 189 through 204
    Processing helix  chain 'A' and resid 213 through 217
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 248 through 265
    Processing helix  chain 'A' and resid 277 through 282
    Processing helix  chain 'A' and resid 303 through 310
      removed outlier: 3.639A  pdb=" N   TYR A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 330
    Processing helix  chain 'A' and resid 336 through 346
    Processing helix  chain 'A' and resid 388 through 405
      removed outlier: 3.512A  pdb=" N   GLN A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   CYS A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 429
    Processing helix  chain 'A' and resid 438 through 478
      Proline residue:  A 460  - end of helix
      Proline residue:  A 466  - end of helix
      removed outlier: 3.764A  pdb=" N   ASN A 478 " --> pdb=" O   ARG A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 510
      removed outlier: 3.907A  pdb=" N   TYR A 486 " --> pdb=" O   SER A 482 " (cutoff:3.500A)
      Proline residue:  A 496  - end of helix
      Proline residue:  A 502  - end of helix
      removed outlier: 4.006A  pdb=" N   ILE A 508 " --> pdb=" O   ALA A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 546
    Processing helix  chain 'A' and resid 549 through 567
      removed outlier: 3.582A  pdb=" N   ALA A 553 " --> pdb=" O   SER A 549 " (cutoff:3.500A)
      Proline residue:  A 558  - end of helix
      Proline residue:  A 563  - end of helix
      removed outlier: 3.655A  pdb=" N   LEU A 566 " --> pdb=" O   ILE A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 587
      removed outlier: 4.241A  pdb=" N   TRP A 583 " --> pdb=" O   THR A 579 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   MET A 584 " --> pdb=" O   TYR A 580 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER A 585 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 602
    Processing helix  chain 'A' and resid 623 through 629
    Processing helix  chain 'A' and resid 635 through 666
      removed outlier: 3.731A  pdb=" N   ASP A 639 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 131
    Processing helix  chain 'B' and resid 154 through 157
    Processing helix  chain 'B' and resid 173 through 186
    Processing helix  chain 'B' and resid 189 through 204
    Processing helix  chain 'B' and resid 213 through 217
    Processing helix  chain 'B' and resid 218 through 231
    Processing helix  chain 'B' and resid 248 through 265
    Processing helix  chain 'B' and resid 277 through 282
    Processing helix  chain 'B' and resid 303 through 310
      removed outlier: 3.639A  pdb=" N   TYR B 307 " --> pdb=" O   ASN B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 320 through 330
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 388 through 405
      removed outlier: 3.512A  pdb=" N   GLN B 392 " --> pdb=" O   SER B 388 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   CYS B 394 " --> pdb=" O   LEU B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 429
    Processing helix  chain 'B' and resid 438 through 478
      Proline residue:  B 460  - end of helix
      Proline residue:  B 466  - end of helix
      removed outlier: 3.764A  pdb=" N   ASN B 478 " --> pdb=" O   ARG B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 510
      removed outlier: 3.907A  pdb=" N   TYR B 486 " --> pdb=" O   SER B 482 " (cutoff:3.500A)
      Proline residue:  B 496  - end of helix
      Proline residue:  B 502  - end of helix
      removed outlier: 4.006A  pdb=" N   ILE B 508 " --> pdb=" O   ALA B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 546
    Processing helix  chain 'B' and resid 549 through 567
      removed outlier: 3.582A  pdb=" N   ALA B 553 " --> pdb=" O   SER B 549 " (cutoff:3.500A)
      Proline residue:  B 558  - end of helix
      Proline residue:  B 563  - end of helix
      removed outlier: 3.655A  pdb=" N   LEU B 566 " --> pdb=" O   ILE B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 578 through 587
      removed outlier: 4.242A  pdb=" N   TRP B 583 " --> pdb=" O   THR B 579 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   MET B 584 " --> pdb=" O   TYR B 580 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER B 585 " --> pdb=" O   LEU B 581 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 602
    Processing helix  chain 'B' and resid 623 through 629
    Processing helix  chain 'B' and resid 635 through 666
      removed outlier: 3.731A  pdb=" N   ASP B 639 " --> pdb=" O   LYS B 635 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 101 through 108
      removed outlier: 6.996A  pdb=" N   LYS A 102 " --> pdb=" O   SER A  83 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   SER A  83 " --> pdb=" O   LYS A 102 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   ILE A 104 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG A  80 " --> pdb=" O   ALA A 142 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA A 142 " --> pdb=" O   ARG A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 162
      removed outlier: 6.566A  pdb=" N   CYS A 160 " --> pdb=" O   PHE A 239 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   ASP A 241 " --> pdb=" O   CYS A 160 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE A 162 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A 297 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   SER A 291 " --> pdb=" O   CYS A 295 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   CYS A 295 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 101 through 108
      removed outlier: 6.996A  pdb=" N   LYS B 102 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   SER B  83 " --> pdb=" O   LYS B 102 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   ILE B 104 " --> pdb=" O   ASP B  81 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG B  80 " --> pdb=" O   ALA B 142 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ALA B 142 " --> pdb=" O   ARG B  80 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 162
      removed outlier: 6.567A  pdb=" N   CYS B 160 " --> pdb=" O   PHE B 239 " (cutoff:3.500A)
      removed outlier: 8.104A  pdb=" N   ASP B 241 " --> pdb=" O   CYS B 160 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   ILE B 162 " --> pdb=" O   ASP B 241 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR B 297 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   SER B 291 " --> pdb=" O   CYS B 295 " (cutoff:3.500A)
      removed outlier: 5.196A  pdb=" N   CYS B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)

    486 hydrogen bonds defined for protein.
    1422 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: 1.06

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2700
        1.34 -     1.46: 1937
        1.46 -     1.58: 4215
        1.58 -     1.69: 0
        1.69 -     1.81: 110
  Bond restraints: 8962
  Sorted by residual:
  bond pdb=" C   ILE A 562 "
       pdb=" N   PRO A 563 "
    ideal  model  delta    sigma   weight residual
    1.337  1.357 -0.020 9.80e-03 1.04e+04 4.13e+00
  bond pdb=" C   ILE B 562 "
       pdb=" N   PRO B 563 "
    ideal  model  delta    sigma   weight residual
    1.337  1.356 -0.019 9.80e-03 1.04e+04 3.84e+00
  bond pdb=" C3  CLR A 801 "
       pdb=" O1  CLR A 801 "
    ideal  model  delta    sigma   weight residual
    1.413  1.392  0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C3  CLR B 703 "
       pdb=" O1  CLR B 703 "
    ideal  model  delta    sigma   weight residual
    1.413  1.392  0.021 2.00e-02 2.50e+03 1.13e+00
  bond pdb=" C3  CLR B 701 "
       pdb=" O1  CLR B 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.392  0.021 2.00e-02 2.50e+03 1.12e+00
  ... (remaining 8957 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 11737
        1.49 -     2.97: 323
        2.97 -     4.46: 53
        4.46 -     5.95: 33
        5.95 -     7.44: 16
  Bond angle restraints: 12162
  Sorted by residual:
  angle pdb=" C   GLN B 620 "
        pdb=" N   LYS B 621 "
        pdb=" CA  LYS B 621 "
      ideal   model   delta    sigma   weight residual
     121.54  127.56   -6.02 1.91e+00 2.74e-01 9.93e+00
  angle pdb=" C   GLN A 620 "
        pdb=" N   LYS A 621 "
        pdb=" CA  LYS A 621 "
      ideal   model   delta    sigma   weight residual
     121.54  127.54   -6.00 1.91e+00 2.74e-01 9.86e+00
  angle pdb=" N   GLY A 299 "
        pdb=" CA  GLY A 299 "
        pdb=" C   GLY A 299 "
      ideal   model   delta    sigma   weight residual
     110.38  114.70   -4.32 1.42e+00 4.96e-01 9.27e+00
  angle pdb=" N   GLY B 299 "
        pdb=" CA  GLY B 299 "
        pdb=" C   GLY B 299 "
      ideal   model   delta    sigma   weight residual
     110.38  114.69   -4.31 1.42e+00 4.96e-01 9.21e+00
  angle pdb=" C13 CLR B 701 "
        pdb=" C17 CLR B 701 "
        pdb=" C20 CLR B 701 "
      ideal   model   delta    sigma   weight residual
     119.60  112.16    7.44 3.00e+00 1.11e-01 6.14e+00
  ... (remaining 12157 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 4712
       17.52 -    35.04: 430
       35.04 -    52.56: 94
       52.56 -    70.07: 14
       70.07 -    87.59: 12
  Dihedral angle restraints: 5262
    sinusoidal: 2116
      harmonic: 3146
  Sorted by residual:
  dihedral pdb=" CB  GLU B 628 "
           pdb=" CG  GLU B 628 "
           pdb=" CD  GLU B 628 "
           pdb=" OE1 GLU B 628 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.59  -87.59     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" CB  GLU A 628 "
           pdb=" CG  GLU A 628 "
           pdb=" CD  GLU A 628 "
           pdb=" OE1 GLU A 628 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.55  -87.55     1      3.00e+01 1.11e-03 1.02e+01
  dihedral pdb=" N   LEU B 636 "
           pdb=" CA  LEU B 636 "
           pdb=" CB  LEU B 636 "
           pdb=" CG  LEU B 636 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.23  -59.77     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5259 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1300
       0.072 -    0.144: 94
       0.144 -    0.215: 3
       0.215 -    0.287: 15
       0.287 -    0.359: 8
  Chirality restraints: 1420
  Sorted by residual:
  chirality pdb=" C14 CLR A 804 "
            pdb=" C13 CLR A 804 "
            pdb=" C15 CLR A 804 "
            pdb=" C8  CLR A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.68    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C14 CLR B 701 "
            pdb=" C13 CLR B 701 "
            pdb=" C15 CLR B 701 "
            pdb=" C8  CLR B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.68    0.36 2.00e-01 2.50e+01 3.22e+00
  chirality pdb=" C14 CLR B 702 "
            pdb=" C13 CLR B 702 "
            pdb=" C15 CLR B 702 "
            pdb=" C8  CLR B 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.67    0.35 2.00e-01 2.50e+01 3.12e+00
  ... (remaining 1417 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 465 "   -0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A 466 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 466 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 466 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 465 "    0.025 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO B 466 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 466 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 466 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 416 "    0.005 2.00e-02 2.50e+03   1.01e-02 1.03e+00
        pdb=" C   THR B 416 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   THR B 416 "    0.007 2.00e-02 2.50e+03
        pdb=" N   SER B 417 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 688
        2.74 -     3.28: 8712
        3.28 -     3.82: 14454
        3.82 -     4.36: 16851
        4.36 -     4.90: 30052
  Nonbonded interactions: 70757
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 404 "
            pdb=" OG1 THR A 411 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   ILE B 404 "
            pdb=" OG1 THR B 411 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OE1 GLN B 164 "
            pdb=" OE1 GLN B 242 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OE1 GLN A 164 "
            pdb=" OE1 GLN A 242 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   SER A 386 "
            pdb=" OG  SER A 386 "
     model   vdw
     2.243 3.040
  ... (remaining 70752 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:             1.090
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     8.180
  Find NCS groups from input model:        0.040
  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:             0.010
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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   0.021   8964  Z= 0.129
  Angle     :  0.655   7.436  12166  Z= 0.339
  Chirality :  0.052   0.359   1420
  Planarity :  0.003   0.037   1474
  Dihedral  : 14.464  87.593   3240
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 11.16 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.24), residues: 1078
  helix:  0.39 (0.20), residues: 620
  sheet: -0.65 (0.53), residues: 78
  loop : -2.83 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 150 
 TYR   0.005   0.001   TYR A 510 
 PHE   0.006   0.001   PHE A 570 
 TRP   0.001   0.000   TRP B 480 
 HIS   0.001   0.000   HIS B 618 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00220 /  0.13 ( 8962)
  covalent geometry    : angle       0.65492 /  0.34 (12162)
  SS BOND              : bond        0.00057 /  0.03 (    2)
  SS BOND              : angle       0.84988 /  0.44 (    4)
  hydrogen bonds       : bond        0.10340 /  7.55 (  486)
  hydrogen bonds       : angle       4.75071 /  3.36 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 194
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7231 (m-30) cc_final: 0.6919 (m-30)
REVERT: A  198 LYS cc_start: 0.8073 (tttp) cc_final: 0.7721 (ttpt)
REVERT: A  618 HIS cc_start: 0.7980 (t70) cc_final: 0.7528 (t-170)
REVERT: A  659 ARG cc_start: 0.7024 (ttt-90) cc_final: 0.6703 (ttm170)
REVERT: B  166 ASP cc_start: 0.7197 (m-30) cc_final: 0.6914 (m-30)
REVERT: B  198 LYS cc_start: 0.8046 (tttp) cc_final: 0.7744 (ttpt)
REVERT: B  618 HIS cc_start: 0.7984 (t70) cc_final: 0.7497 (t-170)
REVERT: B  659 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6700 (ttm170)
  outliers start: 18
  outliers final: 14
  residues processed: 204
  average time/residue: 0.0908
  time to fit residues: 25.5060
Evaluate side-chains
  158 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  445 PHE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  445 PHE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  636 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 336 GLN
A 392 GLN
A 620 GLN
B 336 GLN
** B 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 620 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.119930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.094187 restraints weight = 10219.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.99
r_work: 0.2832 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.1487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8964  Z= 0.173
  Angle     :  0.588   5.631  12166  Z= 0.289
  Chirality :  0.041   0.148   1420
  Planarity :  0.004   0.045   1474
  Dihedral  :  6.163  59.739   1280
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 13.09 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.26), residues: 1078
  helix:  1.07 (0.21), residues: 644
  sheet: -0.54 (0.51), residues: 78
  loop : -2.33 (0.31), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 156 
 TYR   0.012   0.001   TYR B 602 
 PHE   0.016   0.002   PHE B 570 
 TRP   0.004   0.001   TRP B 583 
 HIS   0.003   0.001   HIS B 183 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.17 ( 8962)
  covalent geometry    : angle       0.58847 /  0.29 (12162)
  SS BOND              : bond        0.00033 /  0.02 (    2)
  SS BOND              : angle       0.09529 /  0.05 (    4)
  hydrogen bonds       : bond        0.03664 /  2.48 (  486)
  hydrogen bonds       : angle       3.99362 /  2.83 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 129
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7432 (m-30) cc_final: 0.7054 (m-30)
REVERT: A  198 LYS cc_start: 0.8194 (tttp) cc_final: 0.7672 (ttpt)
REVERT: A  285 ASP cc_start: 0.8582 (m-30) cc_final: 0.8360 (m-30)
REVERT: A  568 SER cc_start: 0.8873 (t) cc_final: 0.8646 (t)
REVERT: A  584 MET cc_start: 0.8176 (mtt) cc_final: 0.7896 (mtt)
REVERT: A  591 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7512 (ttt-90)
REVERT: A  659 ARG cc_start: 0.7368 (ttt-90) cc_final: 0.6870 (ttm170)
REVERT: B  166 ASP cc_start: 0.7438 (m-30) cc_final: 0.6998 (m-30)
REVERT: B  198 LYS cc_start: 0.8189 (tttp) cc_final: 0.7725 (ttpt)
REVERT: B  568 SER cc_start: 0.8889 (t) cc_final: 0.8664 (t)
REVERT: B  584 MET cc_start: 0.8086 (mtt) cc_final: 0.7837 (mtt)
REVERT: B  591 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7529 (ttt-90)
REVERT: B  618 HIS cc_start: 0.8000 (t70) cc_final: 0.7734 (t-170)
REVERT: B  659 ARG cc_start: 0.7409 (ttt-90) cc_final: 0.6885 (ttm170)
  outliers start: 46
  outliers final: 30
  residues processed: 162
  average time/residue: 0.0852
  time to fit residues: 19.3244
Evaluate side-chains
  160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  405 MET
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  632 GLU
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 91 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 92 optimal weight:    0.6980
   chunk 62 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 GLN ** 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 = 0.3313 r_free = 0.3313 target = 0.121957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.096216 restraints weight = 10054.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 2.00
r_work: 0.2895 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8964  Z= 0.110
  Angle     :  0.510   6.030  12166  Z= 0.251
  Chirality :  0.038   0.138   1420
  Planarity :  0.003   0.043   1474
  Dihedral  :  5.505  58.103   1272
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 14.27 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.27), residues: 1078
  helix:  1.44 (0.22), residues: 648
  sheet: -0.24 (0.53), residues: 78
  loop : -2.05 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 651 
 TYR   0.008   0.001   TYR A 602 
 PHE   0.011   0.001   PHE B 570 
 TRP   0.005   0.001   TRP A 583 
 HIS   0.002   0.000   HIS A 618 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.11 ( 8962)
  covalent geometry    : angle       0.51019 /  0.25 (12162)
  SS BOND              : bond        0.00015 /  0.01 (    2)
  SS BOND              : angle       0.26714 /  0.14 (    4)
  hydrogen bonds       : bond        0.03151 /  2.12 (  486)
  hydrogen bonds       : angle       3.79306 /  2.69 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 134
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.7398 (m-30) cc_final: 0.6982 (m-30)
REVERT: A  198 LYS cc_start: 0.8250 (tttp) cc_final: 0.7726 (ttpt)
REVERT: A  285 ASP cc_start: 0.8600 (m-30) cc_final: 0.8358 (m-30)
REVERT: A  568 SER cc_start: 0.8761 (t) cc_final: 0.8526 (t)
REVERT: A  584 MET cc_start: 0.8208 (mtt) cc_final: 0.7922 (mtt)
REVERT: A  591 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7603 (tmt-80)
REVERT: A  659 ARG cc_start: 0.7418 (ttt-90) cc_final: 0.6960 (ttm170)
REVERT: B  166 ASP cc_start: 0.7398 (m-30) cc_final: 0.6970 (m-30)
REVERT: B  198 LYS cc_start: 0.8253 (tttp) cc_final: 0.7779 (ttpt)
REVERT: B  568 SER cc_start: 0.8770 (t) cc_final: 0.8537 (t)
REVERT: B  584 MET cc_start: 0.8124 (mtt) cc_final: 0.7845 (mtt)
REVERT: B  591 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7598 (tmt-80)
REVERT: B  618 HIS cc_start: 0.8129 (t70) cc_final: 0.7824 (t-170)
REVERT: B  659 ARG cc_start: 0.7422 (ttt-90) cc_final: 0.6943 (ttm170)
  outliers start: 37
  outliers final: 28
  residues processed: 157
  average time/residue: 0.0764
  time to fit residues: 17.3934
Evaluate side-chains
  157 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  514 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  632 GLU
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 88 optimal weight:    0.8980
   chunk 60 optimal weight:    6.9990
   chunk 102 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 95 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 GLN ** 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 = 0.3302 r_free = 0.3302 target = 0.121077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.095988 restraints weight = 10219.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.89
r_work: 0.2863 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8964  Z= 0.112
  Angle     :  0.505   6.027  12166  Z= 0.248
  Chirality :  0.038   0.138   1420
  Planarity :  0.003   0.043   1474
  Dihedral  :  5.227  57.585   1270
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 14.91 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.27), residues: 1078
  helix:  1.63 (0.22), residues: 650
  sheet: -0.02 (0.55), residues: 78
  loop : -1.87 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 651 
 TYR   0.008   0.001   TYR A 602 
 PHE   0.012   0.001   PHE B 570 
 TRP   0.004   0.001   TRP A 583 
 HIS   0.002   0.001   HIS A 618 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.11 ( 8962)
  covalent geometry    : angle       0.50514 /  0.25 (12162)
  SS BOND              : bond        0.00004 /  0.00 (    2)
  SS BOND              : angle       0.16395 /  0.08 (    4)
  hydrogen bonds       : bond        0.03102 /  2.09 (  486)
  hydrogen bonds       : angle       3.67093 /  2.59 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 133
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  166 ASP cc_start: 0.7323 (m-30) cc_final: 0.6896 (m-30)
REVERT: A  198 LYS cc_start: 0.8165 (tttp) cc_final: 0.7642 (ttpt)
REVERT: A  285 ASP cc_start: 0.8588 (m-30) cc_final: 0.8322 (m-30)
REVERT: A  568 SER cc_start: 0.8867 (t) cc_final: 0.8630 (t)
REVERT: A  584 MET cc_start: 0.8029 (mtt) cc_final: 0.7730 (mtt)
REVERT: A  591 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7605 (tmt-80)
REVERT: A  659 ARG cc_start: 0.7306 (ttt-90) cc_final: 0.6840 (ttm170)
REVERT: B  166 ASP cc_start: 0.7329 (m-30) cc_final: 0.6886 (m-30)
REVERT: B  198 LYS cc_start: 0.8159 (tttp) cc_final: 0.7680 (ttpt)
REVERT: B  568 SER cc_start: 0.8859 (t) cc_final: 0.8622 (t)
REVERT: B  584 MET cc_start: 0.8035 (mtt) cc_final: 0.7729 (mtt)
REVERT: B  591 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7625 (tmt-80)
REVERT: B  618 HIS cc_start: 0.8146 (t70) cc_final: 0.7823 (t-170)
REVERT: B  659 ARG cc_start: 0.7327 (ttt-90) cc_final: 0.6838 (ttm170)
  outliers start: 45
  outliers final: 31
  residues processed: 164
  average time/residue: 0.0827
  time to fit residues: 19.5828
Evaluate side-chains
  160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  613 ILE
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 80 optimal weight:    8.9990
   chunk 10 optimal weight:    4.9990
   chunk 90 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 392 GLN ** 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 = 0.3268 r_free = 0.3268 target = 0.118388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.092607 restraints weight = 10237.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.00
r_work: 0.2844 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2702 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8964  Z= 0.150
  Angle     :  0.545   6.252  12166  Z= 0.266
  Chirality :  0.040   0.140   1420
  Planarity :  0.004   0.043   1474
  Dihedral  :  5.439  59.301   1270
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 15.13 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.27), residues: 1078
  helix:  1.48 (0.21), residues: 658
  sheet:  0.07 (0.55), residues: 78
  loop : -1.78 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 651 
 TYR   0.010   0.001   TYR B 592 
 PHE   0.014   0.001   PHE A 570 
 TRP   0.003   0.001   TRP A 480 
 HIS   0.002   0.001   HIS B 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.15 ( 8962)
  covalent geometry    : angle       0.54541 /  0.27 (12162)
  SS BOND              : bond        0.00012 /  0.01 (    2)
  SS BOND              : angle       0.07796 /  0.04 (    4)
  hydrogen bonds       : bond        0.03446 /  2.33 (  486)
  hydrogen bonds       : angle       3.78822 /  2.66 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 130
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7416 (m-30) cc_final: 0.6973 (m-30)
REVERT: A  198 LYS cc_start: 0.8277 (tttp) cc_final: 0.7754 (ttpt)
REVERT: A  285 ASP cc_start: 0.8644 (m-30) cc_final: 0.8386 (m-30)
REVERT: A  591 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7677 (tmt-80)
REVERT: A  659 ARG cc_start: 0.7489 (ttt-90) cc_final: 0.7013 (ttm170)
REVERT: B  166 ASP cc_start: 0.7400 (m-30) cc_final: 0.6947 (m-30)
REVERT: B  198 LYS cc_start: 0.8253 (tttp) cc_final: 0.7756 (ttpt)
REVERT: B  584 MET cc_start: 0.8195 (mtt) cc_final: 0.7912 (mtt)
REVERT: B  591 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7691 (tmt-80)
REVERT: B  618 HIS cc_start: 0.8255 (t70) cc_final: 0.7968 (t-170)
REVERT: B  659 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.6979 (ttm170)
  outliers start: 48
  outliers final: 34
  residues processed: 159
  average time/residue: 0.0862
  time to fit residues: 19.8462
Evaluate side-chains
  160 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  469 MET
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  632 GLU
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.7988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 337 ASN
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 GLN ** 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 = 0.3233 r_free = 0.3233 target = 0.115887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.090314 restraints weight = 10328.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 1.99
r_work: 0.2826 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8714
moved from start:          0.2117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8964  Z= 0.193
  Angle     :  0.593   6.750  12166  Z= 0.288
  Chirality :  0.042   0.139   1420
  Planarity :  0.004   0.046   1474
  Dihedral  :  5.675  58.302   1270
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 14.91 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.27), residues: 1078
  helix:  1.37 (0.21), residues: 656
  sheet:  0.04 (0.54), residues: 78
  loop : -1.81 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 222 
 TYR   0.011   0.001   TYR A 592 
 PHE   0.013   0.001   PHE A 465 
 TRP   0.005   0.001   TRP A 480 
 HIS   0.003   0.001   HIS A 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00478 /  0.19 ( 8962)
  covalent geometry    : angle       0.59319 /  0.29 (12162)
  SS BOND              : bond        0.00011 /  0.01 (    2)
  SS BOND              : angle       0.01010 /  0.00 (    4)
  hydrogen bonds       : bond        0.03773 /  2.55 (  486)
  hydrogen bonds       : angle       3.91712 /  2.75 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 123
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7453 (m-30) cc_final: 0.7006 (m-30)
REVERT: A  198 LYS cc_start: 0.8196 (tttp) cc_final: 0.7683 (ttpt)
REVERT: A  285 ASP cc_start: 0.8695 (m-30) cc_final: 0.8447 (m-30)
REVERT: A  591 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7723 (ttt-90)
REVERT: A  628 GLU cc_start: 0.8230 (tp30) cc_final: 0.7904 (tp30)
REVERT: A  659 ARG cc_start: 0.7505 (ttt-90) cc_final: 0.7046 (ttm170)
REVERT: B  166 ASP cc_start: 0.7424 (m-30) cc_final: 0.6964 (m-30)
REVERT: B  198 LYS cc_start: 0.8237 (tttp) cc_final: 0.7725 (ttpt)
REVERT: B  591 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7734 (ttt-90)
REVERT: B  618 HIS cc_start: 0.8212 (t70) cc_final: 0.8006 (t-170)
REVERT: B  628 GLU cc_start: 0.8226 (tp30) cc_final: 0.7807 (tp30)
REVERT: B  659 ARG cc_start: 0.7504 (ttt-90) cc_final: 0.7025 (ttm170)
  outliers start: 59
  outliers final: 40
  residues processed: 163
  average time/residue: 0.0818
  time to fit residues: 19.4317
Evaluate side-chains
  162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  139 MET
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  391 THR
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  508 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  520 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  469 MET
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  508 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  520 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  568 SER
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0870
   overall best weight:    0.7160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 GLN ** 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 = 0.3282 r_free = 0.3282 target = 0.119792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.094981 restraints weight = 10202.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 1.85
r_work: 0.2849 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8964  Z= 0.109
  Angle     :  0.522   7.410  12166  Z= 0.255
  Chirality :  0.038   0.138   1420
  Planarity :  0.003   0.044   1474
  Dihedral  :  5.484  57.807   1270
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 16.85 %
    Favored  : 78.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.27), residues: 1078
  helix:  1.70 (0.21), residues: 652
  sheet:  0.15 (0.54), residues: 78
  loop : -1.65 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 339 
 TYR   0.007   0.001   TYR B 602 
 PHE   0.010   0.001   PHE B 570 
 TRP   0.004   0.001   TRP A 583 
 HIS   0.003   0.000   HIS A 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.11 ( 8962)
  covalent geometry    : angle       0.52185 /  0.26 (12162)
  SS BOND              : bond        0.00039 /  0.02 (    2)
  SS BOND              : angle       0.09318 /  0.04 (    4)
  hydrogen bonds       : bond        0.03175 /  2.13 (  486)
  hydrogen bonds       : angle       3.70762 /  2.61 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 0.266 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7280 (m-30) cc_final: 0.6831 (m-30)
REVERT: A  198 LYS cc_start: 0.8054 (tttp) cc_final: 0.7541 (ttpt)
REVERT: A  285 ASP cc_start: 0.8614 (m-30) cc_final: 0.8325 (m-30)
REVERT: A  591 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7646 (tmt-80)
REVERT: A  659 ARG cc_start: 0.7263 (ttt-90) cc_final: 0.6778 (ttm170)
REVERT: B  166 ASP cc_start: 0.7269 (m-30) cc_final: 0.6811 (m-30)
REVERT: B  198 LYS cc_start: 0.8092 (tttp) cc_final: 0.7579 (ttpt)
REVERT: B  584 MET cc_start: 0.7917 (mtt) cc_final: 0.7656 (mtt)
REVERT: B  591 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7640 (tmt-80)
REVERT: B  618 HIS cc_start: 0.8199 (t70) cc_final: 0.7964 (t-170)
REVERT: B  628 GLU cc_start: 0.7998 (tp30) cc_final: 0.7682 (tp30)
REVERT: B  659 ARG cc_start: 0.7267 (ttt-90) cc_final: 0.6773 (ttm170)
  outliers start: 42
  outliers final: 31
  residues processed: 154
  average time/residue: 0.0878
  time to fit residues: 19.5016
Evaluate side-chains
  156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  632 GLU
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 GLN ** 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 = 0.3224 r_free = 0.3224 target = 0.115289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.089695 restraints weight = 10368.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.02
r_work: 0.2807 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2664 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8964  Z= 0.211
  Angle     :  0.629   7.621  12166  Z= 0.302
  Chirality :  0.043   0.141   1420
  Planarity :  0.004   0.045   1474
  Dihedral  :  5.631  54.970   1269
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 17.27 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.27), residues: 1078
  helix:  1.44 (0.21), residues: 650
  sheet: -0.08 (0.53), residues: 78
  loop : -1.71 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 339 
 TYR   0.010   0.001   TYR A 592 
 PHE   0.014   0.002   PHE B 465 
 TRP   0.006   0.001   TRP A 480 
 HIS   0.004   0.001   HIS B 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00528 /  0.21 ( 8962)
  covalent geometry    : angle       0.62879 /  0.30 (12162)
  SS BOND              : bond        0.00003 /  0.00 (    2)
  SS BOND              : angle       0.06843 /  0.04 (    4)
  hydrogen bonds       : bond        0.03918 /  2.65 (  486)
  hydrogen bonds       : angle       3.95484 /  2.77 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7445 (m-30) cc_final: 0.6999 (m-30)
REVERT: A  198 LYS cc_start: 0.8171 (tttp) cc_final: 0.7649 (ttpt)
REVERT: A  285 ASP cc_start: 0.8709 (m-30) cc_final: 0.8430 (m-30)
REVERT: A  591 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7751 (ttt-90)
REVERT: A  659 ARG cc_start: 0.7482 (ttt-90) cc_final: 0.7024 (ttm170)
REVERT: B  166 ASP cc_start: 0.7411 (m-30) cc_final: 0.6954 (m-30)
REVERT: B  198 LYS cc_start: 0.8172 (tttp) cc_final: 0.7660 (ttpt)
REVERT: B  591 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7736 (ttt-90)
REVERT: B  618 HIS cc_start: 0.8219 (t70) cc_final: 0.8016 (t-170)
REVERT: B  628 GLU cc_start: 0.8190 (tp30) cc_final: 0.7872 (tp30)
REVERT: B  659 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.7008 (ttm170)
  outliers start: 42
  outliers final: 34
  residues processed: 150
  average time/residue: 0.0817
  time to fit residues: 17.7924
Evaluate side-chains
  155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  469 MET
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  564 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 39 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 392 GLN ** 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 = 0.3257 r_free = 0.3257 target = 0.117926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.092601 restraints weight = 10198.905|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 1.98
r_work: 0.2810 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8964  Z= 0.134
  Angle     :  0.558   8.190  12166  Z= 0.270
  Chirality :  0.039   0.139   1420
  Planarity :  0.004   0.045   1474
  Dihedral  :  5.502  54.507   1269
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.70 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 1078
  helix:  1.62 (0.21), residues: 654
  sheet:  0.07 (0.54), residues: 78
  loop : -1.60 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 339 
 TYR   0.008   0.001   TYR B 429 
 PHE   0.011   0.001   PHE A 570 
 TRP   0.005   0.001   TRP A 583 
 HIS   0.003   0.001   HIS B 171 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.13 ( 8962)
  covalent geometry    : angle       0.55802 /  0.27 (12162)
  SS BOND              : bond        0.00025 /  0.01 (    2)
  SS BOND              : angle       0.09948 /  0.05 (    4)
  hydrogen bonds       : bond        0.03409 /  2.29 (  486)
  hydrogen bonds       : angle       3.81309 /  2.68 ( 1422)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7380 (m-30) cc_final: 0.6930 (m-30)
REVERT: A  198 LYS cc_start: 0.8159 (tttp) cc_final: 0.7643 (ttpt)
REVERT: A  285 ASP cc_start: 0.8674 (m-30) cc_final: 0.8398 (m-30)
REVERT: A  591 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7744 (tmt-80)
REVERT: A  659 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.6933 (ttm170)
REVERT: B  166 ASP cc_start: 0.7321 (m-30) cc_final: 0.6864 (m-30)
REVERT: B  198 LYS cc_start: 0.8125 (tttp) cc_final: 0.7606 (ttpt)
REVERT: B  591 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7724 (tmt-80)
REVERT: B  628 GLU cc_start: 0.8072 (tp30) cc_final: 0.7746 (tp30)
REVERT: B  659 ARG cc_start: 0.7428 (ttt-90) cc_final: 0.6931 (ttm170)
  outliers start: 36
  outliers final: 32
  residues processed: 143
  average time/residue: 0.0855
  time to fit residues: 17.8060
Evaluate side-chains
  155 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 121
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  143 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  432 ILE
Chi-restraints excluded: chain A residue  509 VAL
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  591 ARG
Chi-restraints excluded: chain A residue  665 GLU
Chi-restraints excluded: chain B residue  114 VAL
Chi-restraints excluded: chain B residue  139 MET
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  389 CYS
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  509 VAL
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  559 VAL
Chi-restraints excluded: chain B residue  591 ARG
Chi-restraints excluded: chain B residue  617 CYS
Chi-restraints excluded: chain B residue  665 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program
    task.run()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__
    ro.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__
    refiner.refine(
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run
    return run_c_plus_plus(
           ^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites
    pair_proxies = self.pair_proxies(
                   ^^^^^^^^^^^^^^^^^^
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2068 > 50:
  distance: 31 - 197:  20.840
  distance: 34 - 210:  20.172
  distance: 43 - 213:  21.204
  distance: 84 - 191:  18.915
  distance: 87 - 202:  22.773
  distance: 101 - 205:  24.302
  distance: 104 - 216:  30.872
  distance: 138 - 160:  17.891
  distance: 146 - 169:  29.687
  distance: 157 - 160:  14.310
  distance: 160 - 161:   5.397
  distance: 161 - 162:  43.615
  distance: 161 - 164:  20.899
  distance: 162 - 163:  56.129
  distance: 164 - 165:  20.651
  distance: 165 - 166:   7.873
  distance: 166 - 167:   8.275
  distance: 166 - 168:   5.852
  distance: 169 - 170:   6.976
  distance: 170 - 171:  38.258
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