Starting phenix.real_space_refine
on Fri Mar 14 02:38:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur3_42480/03_2025/8ur3_42480.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
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      44      5.16       5
     C    5982      2.51       5
     N    1544      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9376
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4688
          Classifications: {'peptide': 579}
          Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 579, 4688
          Classifications: {'peptide': 579}
          Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555}
          Chain breaks: 1
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N   ARG A  78 " occ=0.86
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  78 " occ=0.86
    residue:
      pdb=" N   GLY A  79 " occ=0.82
      ... (2 atoms not shown)
      pdb=" O   GLY A  79 " occ=0.82
    residue:
      pdb=" N   GLY A  80 " occ=0.83
      ... (2 atoms not shown)
      pdb=" O   GLY A  80 " occ=0.83
    residue:
      pdb=" N   ARG A  81 " occ=0.62
      ... (9 atoms not shown)
      pdb=" NH2 ARG A  81 " occ=0.62
    residue:
      pdb=" N   ARG B  78 " occ=0.86
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  78 " occ=0.86
    residue:
      pdb=" N   GLY B  79 " occ=0.82
      ... (2 atoms not shown)
      pdb=" O   GLY B  79 " occ=0.82
    residue:
      pdb=" N   GLY B  80 " occ=0.83
      ... (2 atoms not shown)
      pdb=" O   GLY B  80 " occ=0.83
    residue:
      pdb=" N   ARG B  81 " occ=0.62
      ... (9 atoms not shown)
      pdb=" NH2 ARG B  81 " occ=0.62
  Time building chain proxies: 6.26, per 1000 atoms: 0.67
  Number of scatterers: 9376
  At special positions: 0
  Unit cell: (101.268, 115.884, 82.476, 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      44     16.00
     O    1806      8.00
     N    1544      7.00
     C    5982      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 8 sheets defined
      42.7% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 12
      removed outlier: 3.536A  pdb=" N   ALA A  10 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 23
      removed outlier: 3.519A  pdb=" N   ASN A  22 " --> pdb=" O   ASN A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 44
    Processing helix  chain 'A' and resid 48 through 50
      No H-bonds generated for 'chain 'A' and resid 48 through 50'
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 106 through 118
    Processing helix  chain 'A' and resid 143 through 155
    Processing helix  chain 'A' and resid 158 through 162
      removed outlier: 3.991A  pdb=" N   ASP A 162 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 176
      removed outlier: 3.596A  pdb=" N   PHE A 175 " --> pdb=" O   SER A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.571A  pdb=" N   ILE A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR A 185 " --> pdb=" O   ILE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 205
    Processing helix  chain 'A' and resid 206 through 209
      removed outlier: 3.771A  pdb=" N   ILE A 209 " --> pdb=" O   VAL A 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 206 through 209'
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 229 through 240
      removed outlier: 3.533A  pdb=" N   HIS A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 324
    Processing helix  chain 'A' and resid 326 through 331
      removed outlier: 3.670A  pdb=" N   GLY A 330 " --> pdb=" O   PRO A 327 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   ASN A 331 " --> pdb=" O   GLU A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 337
    Processing helix  chain 'A' and resid 354 through 366
    Processing helix  chain 'A' and resid 426 through 430
    Processing helix  chain 'A' and resid 431 through 443
    Processing helix  chain 'A' and resid 449 through 456
      removed outlier: 3.643A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 454 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 523
      removed outlier: 3.584A  pdb=" N   SER A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 537
    Processing helix  chain 'A' and resid 538 through 550
      removed outlier: 3.682A  pdb=" N   ASN A 550 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 562 through 576
    Processing helix  chain 'A' and resid 579 through 588
    Processing helix  chain 'B' and resid 6 through 12
      removed outlier: 3.536A  pdb=" N   ALA B  10 " --> pdb=" O   GLY B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 23
      removed outlier: 3.521A  pdb=" N   ASN B  22 " --> pdb=" O   ASN B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 44
    Processing helix  chain 'B' and resid 48 through 50
      No H-bonds generated for 'chain 'B' and resid 48 through 50'
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 106 through 118
    Processing helix  chain 'B' and resid 143 through 155
    Processing helix  chain 'B' and resid 158 through 162
      removed outlier: 3.988A  pdb=" N   ASP B 162 " --> pdb=" O   GLU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 176
      removed outlier: 3.593A  pdb=" N   PHE B 175 " --> pdb=" O   SER B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.571A  pdb=" N   ILE B 181 " --> pdb=" O   SER B 177 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR B 185 " --> pdb=" O   ILE B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 205
    Processing helix  chain 'B' and resid 206 through 209
      removed outlier: 3.771A  pdb=" N   ILE B 209 " --> pdb=" O   VAL B 206 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 206 through 209'
    Processing helix  chain 'B' and resid 224 through 229
    Processing helix  chain 'B' and resid 229 through 240
      removed outlier: 3.525A  pdb=" N   HIS B 240 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 324
    Processing helix  chain 'B' and resid 326 through 331
      removed outlier: 3.663A  pdb=" N   GLY B 330 " --> pdb=" O   PRO B 327 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   ASN B 331 " --> pdb=" O   GLU B 328 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 354 through 366
    Processing helix  chain 'B' and resid 426 through 430
    Processing helix  chain 'B' and resid 431 through 443
    Processing helix  chain 'B' and resid 449 through 456
      removed outlier: 3.640A  pdb=" N   LEU B 453 " --> pdb=" O   LYS B 449 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 454 " --> pdb=" O   ILE B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 523
      removed outlier: 3.584A  pdb=" N   SER B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 537
    Processing helix  chain 'B' and resid 538 through 550
      removed outlier: 3.681A  pdb=" N   ASN B 550 " --> pdb=" O   ILE B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 562 through 576
    Processing helix  chain 'B' and resid 579 through 588
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4
    Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245
      removed outlier: 6.273A  pdb=" N   ILE A  52 " --> pdb=" O   GLN A 243 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   GLU A 245 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   ILE A  54 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ALA A  25 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   LEU A  55 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU A  27 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   THR A 289 " --> pdb=" O   ILE A  28 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL A 286 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   ILE A 494 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL A 288 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133
      removed outlier: 4.384A  pdb=" N   MET A 389 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ALA A 413 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257
      removed outlier: 6.032A  pdb=" N   VAL A 250 " --> pdb=" O   ASP A 270 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ASP A 270 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASP A 252 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLU A 266 " --> pdb=" O   LYS A 254 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ASP A 256 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA A 264 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4
    Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245
      removed outlier: 6.268A  pdb=" N   ILE B  52 " --> pdb=" O   GLN B 243 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   GLU B 245 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   ILE B  54 " --> pdb=" O   GLU B 245 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   ALA B  25 " --> pdb=" O   HIS B  53 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   LEU B  55 " --> pdb=" O   ALA B  25 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU B  27 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   THR B 289 " --> pdb=" O   ILE B  28 " (cutoff:3.500A)
      removed outlier: 8.253A  pdb=" N   ALA B 492 " --> pdb=" O   ASP B 284 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   VAL B 286 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ILE B 494 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL B 288 " --> pdb=" O   ILE B 494 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133
      removed outlier: 4.385A  pdb=" N   MET B 389 " --> pdb=" O   ILE B 382 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA B 413 " --> pdb=" O   VAL B 346 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   VAL B 346 " --> pdb=" O   ALA B 413 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257
      removed outlier: 6.037A  pdb=" N   VAL B 250 " --> pdb=" O   ASP B 270 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   ASP B 270 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ASP B 252 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU B 266 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ASP B 256 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ALA B 264 " --> pdb=" O   ASP B 256 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    951 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.52

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3033
        1.34 -     1.46: 1785
        1.46 -     1.57: 4702
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9592
  Sorted by residual:
  bond pdb=" C   ILE A 581 "
       pdb=" O   ILE A 581 "
    ideal  model  delta    sigma   weight residual
    1.237  1.225  0.013 1.17e-02 7.31e+03 1.15e+00
  bond pdb=" N   ILE A 461 "
       pdb=" CA  ILE A 461 "
    ideal  model  delta    sigma   weight residual
    1.458  1.450  0.008 7.70e-03 1.69e+04 1.02e+00
  bond pdb=" CB  GLU A 110 "
       pdb=" CG  GLU A 110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 9.82e-01
  bond pdb=" CA  ILE A 461 "
       pdb=" C   ILE A 461 "
    ideal  model  delta    sigma   weight residual
    1.528  1.536 -0.008 8.50e-03 1.38e+04 9.33e-01
  bond pdb=" CB  GLU B 110 "
       pdb=" CG  GLU B 110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.491  0.029 3.00e-02 1.11e+03 9.23e-01
  ... (remaining 9587 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 12595
        1.22 -     2.45: 316
        2.45 -     3.67: 65
        3.67 -     4.90: 10
        4.90 -     6.12: 12
  Bond angle restraints: 12998
  Sorted by residual:
  angle pdb=" C   HIS A 588 "
        pdb=" N   LYS A 589 "
        pdb=" CA  LYS A 589 "
      ideal   model   delta    sigma   weight residual
     121.54  127.31   -5.77 1.91e+00 2.74e-01 9.14e+00
  angle pdb=" C   HIS B 588 "
        pdb=" N   LYS B 589 "
        pdb=" CA  LYS B 589 "
      ideal   model   delta    sigma   weight residual
     121.54  127.29   -5.75 1.91e+00 2.74e-01 9.07e+00
  angle pdb=" C   GLN A 396 "
        pdb=" N   GLN A 397 "
        pdb=" CA  GLN A 397 "
      ideal   model   delta    sigma   weight residual
     121.70  126.19   -4.49 1.80e+00 3.09e-01 6.21e+00
  angle pdb=" C   GLN B 396 "
        pdb=" N   GLN B 397 "
        pdb=" CA  GLN B 397 "
      ideal   model   delta    sigma   weight residual
     121.70  126.16   -4.46 1.80e+00 3.09e-01 6.14e+00
  angle pdb=" N   VAL B 169 "
        pdb=" CA  VAL B 169 "
        pdb=" C   VAL B 169 "
      ideal   model   delta    sigma   weight residual
     113.47  111.16    2.31 1.01e+00 9.80e-01 5.25e+00
  ... (remaining 12993 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.66: 5074
       14.66 -    29.33: 498
       29.33 -    43.99: 134
       43.99 -    58.66: 24
       58.66 -    73.32: 16
  Dihedral angle restraints: 5746
    sinusoidal: 2336
      harmonic: 3410
  Sorted by residual:
  dihedral pdb=" CA  VAL B 483 "
           pdb=" C   VAL B 483 "
           pdb=" N   VAL B 484 "
           pdb=" CA  VAL B 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.48   17.52     0      5.00e+00 4.00e-02 1.23e+01
  dihedral pdb=" CA  VAL A 483 "
           pdb=" C   VAL A 483 "
           pdb=" N   VAL A 484 "
           pdb=" CA  VAL A 484 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.62   17.38     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CG  ARG B 540 "
           pdb=" CD  ARG B 540 "
           pdb=" NE  ARG B 540 "
           pdb=" CZ  ARG B 540 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -130.89   40.89     2      1.50e+01 4.44e-03 9.14e+00
  ... (remaining 5743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 771
       0.030 -    0.059: 406
       0.059 -    0.089: 157
       0.089 -    0.119: 60
       0.119 -    0.148: 32
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CB  ILE B 278 "
            pdb=" CA  ILE B 278 "
            pdb=" CG1 ILE B 278 "
            pdb=" CG2 ILE B 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.51e-01
  chirality pdb=" CB  ILE A 278 "
            pdb=" CA  ILE A 278 "
            pdb=" CG1 ILE A 278 "
            pdb=" CG2 ILE A 278 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.18e-01
  chirality pdb=" CA  ILE A 529 "
            pdb=" N   ILE A 529 "
            pdb=" C   ILE A 529 "
            pdb=" CB  ILE A 529 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1423 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 190 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO B 191 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 191 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 191 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 190 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 191 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 191 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 191 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 231 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.44e+00
        pdb=" N   PRO A 232 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 232 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 232 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2281
        2.78 -     3.31: 8750
        3.31 -     3.84: 16605
        3.84 -     4.37: 20500
        4.37 -     4.90: 33708
  Nonbonded interactions: 81844
  Sorted by model distance:
  nonbonded pdb=" O   THR A 185 "
            pdb=" OH  TYR A 412 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   THR B 185 "
            pdb=" OH  TYR B 412 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 431 "
            pdb=" OD1 ASN A 433 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OG  SER B 431 "
            pdb=" OD1 ASN B 433 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OD1 ASP A 301 "
            pdb=" OG1 THR A 304 "
     model   vdw
     2.273 3.040
  ... (remaining 81839 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: 0.05
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=0.62 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:             1.340
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.540
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:26.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
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      :  0.003   0.031   9592  Z= 0.215
  Angle     :  0.513   6.122  12998  Z= 0.274
  Chirality :  0.045   0.148   1426
  Planarity :  0.003   0.030   1668
  Dihedral  : 13.471  73.321   3542
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.23), residues: 1150
  helix: -0.69 (0.23), residues: 388
  sheet:  0.20 (0.47), residues: 142
  loop : -0.26 (0.24), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 208 
 PHE   0.009   0.001   PHE A  11 
 TYR   0.008   0.001   TYR A 464 
 ARG   0.001   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8543 (pm20) cc_final: 0.8293 (pm20)
REVERT: A   19 ASN cc_start: 0.8463 (t0) cc_final: 0.8248 (t0)
REVERT: A  132 GLN cc_start: 0.8494 (mp10) cc_final: 0.7930 (mp10)
REVERT: A  233 MET cc_start: 0.9133 (mtm) cc_final: 0.8891 (mtm)
REVERT: A  261 GLN cc_start: 0.8713 (pt0) cc_final: 0.8181 (pm20)
REVERT: A  401 ASP cc_start: 0.8650 (m-30) cc_final: 0.8080 (t0)
REVERT: A  564 MET cc_start: 0.7545 (mmp) cc_final: 0.6731 (tpt)
REVERT: B   18 GLU cc_start: 0.8538 (pm20) cc_final: 0.8296 (pm20)
REVERT: B   19 ASN cc_start: 0.8466 (t0) cc_final: 0.8250 (t0)
REVERT: B  132 GLN cc_start: 0.8488 (mp10) cc_final: 0.7931 (mp10)
REVERT: B  233 MET cc_start: 0.9148 (mtm) cc_final: 0.8909 (mtm)
REVERT: B  261 GLN cc_start: 0.8710 (pt0) cc_final: 0.8186 (pm20)
REVERT: B  564 MET cc_start: 0.7572 (mmp) cc_final: 0.6684 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 1.6369
  time to fit residues: 197.5026
Evaluate side-chains
  67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.1980
   chunk 89 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 442 HIS
B 442 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.077144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.063601 restraints weight = 20955.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 2.74
r_work: 0.2858 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2863
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2863 r_free = 0.2863    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9592  Z= 0.180
  Angle     :  0.478   4.970  12998  Z= 0.258
  Chirality :  0.044   0.158   1426
  Planarity :  0.003   0.027   1668
  Dihedral  :  4.018  15.329   1252
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.35 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1150
  helix:  0.63 (0.26), residues: 394
  sheet: -0.06 (0.46), residues: 136
  loop : -0.03 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 316 
 HIS   0.001   0.000   HIS B 208 
 PHE   0.012   0.001   PHE A 506 
 TYR   0.014   0.001   TYR A 112 
 ARG   0.003   0.000   ARG A 324 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8640 (pm20) cc_final: 0.8439 (pm20)
REVERT: A  132 GLN cc_start: 0.8538 (mp10) cc_final: 0.7855 (mp10)
REVERT: A  159 GLU cc_start: 0.8913 (mp0) cc_final: 0.8652 (pm20)
REVERT: A  261 GLN cc_start: 0.8661 (pt0) cc_final: 0.8192 (pm20)
REVERT: A  401 ASP cc_start: 0.8651 (m-30) cc_final: 0.8022 (t0)
REVERT: A  564 MET cc_start: 0.7264 (mmp) cc_final: 0.6483 (tpt)
REVERT: B   18 GLU cc_start: 0.8635 (pm20) cc_final: 0.8435 (pm20)
REVERT: B  132 GLN cc_start: 0.8557 (mp10) cc_final: 0.7877 (mp10)
REVERT: B  159 GLU cc_start: 0.8896 (mp0) cc_final: 0.8639 (pm20)
REVERT: B  261 GLN cc_start: 0.8658 (pt0) cc_final: 0.8201 (pm20)
REVERT: B  401 ASP cc_start: 0.8652 (m-30) cc_final: 0.8036 (t0)
REVERT: B  564 MET cc_start: 0.7281 (mmp) cc_final: 0.6547 (tpt)
REVERT: B  574 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8518 (pptt)
REVERT: B  586 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8597 (mttm)
  outliers start: 10
  outliers final: 2
  residues processed: 77
  average time/residue: 1.4113
  time to fit residues: 116.1611
Evaluate side-chains
  66 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 62
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  574 LYS
Chi-restraints excluded: chain B residue  586 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0010
   chunk 3 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0770
   chunk 1 optimal weight:    0.0770
   overall best weight:    0.8304

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.075648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.061933 restraints weight = 21338.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.2990 rms_B_bonded: 2.75
r_work: 0.2832 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2835
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.84   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2835 r_free = 0.2835    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2835
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9592  Z= 0.181
  Angle     :  0.452   4.881  12998  Z= 0.243
  Chirality :  0.043   0.152   1426
  Planarity :  0.003   0.024   1668
  Dihedral  :  3.871  14.968   1252
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.52 %
    Favored  : 89.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1150
  helix:  1.18 (0.27), residues: 394
  sheet: -0.18 (0.45), residues: 138
  loop :  0.18 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 316 
 HIS   0.002   0.001   HIS A 442 
 PHE   0.015   0.001   PHE A 506 
 TYR   0.012   0.001   TYR A 112 
 ARG   0.003   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8556 (mp10) cc_final: 0.7871 (mp10)
REVERT: A  198 MET cc_start: 0.9103 (tpt) cc_final: 0.8688 (tpt)
REVERT: A  564 MET cc_start: 0.7293 (mmp) cc_final: 0.6417 (tmm)
REVERT: B  132 GLN cc_start: 0.8571 (mp10) cc_final: 0.7898 (mp10)
REVERT: B  564 MET cc_start: 0.7330 (mmp) cc_final: 0.6672 (tpt)
  outliers start: 6
  outliers final: 2
  residues processed: 66
  average time/residue: 1.3428
  time to fit residues: 95.7958
Evaluate side-chains
  62 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 1.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  508 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 90 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A 331 ASN
B 240 HIS
B 331 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.058117 restraints weight = 21142.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.67
r_work: 0.2753 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2754
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.87   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2754 r_free = 0.2754    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2754
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   9592  Z= 0.422
  Angle     :  0.546   5.115  12998  Z= 0.296
  Chirality :  0.047   0.146   1426
  Planarity :  0.003   0.024   1668
  Dihedral  :  4.291  15.383   1252
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.10 %
    Favored  : 88.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1150
  helix:  1.32 (0.27), residues: 394
  sheet: -0.43 (0.44), residues: 138
  loop :  0.16 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 316 
 HIS   0.004   0.001   HIS B 442 
 PHE   0.026   0.002   PHE B 506 
 TYR   0.015   0.001   TYR A 226 
 ARG   0.003   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8534 (mp10) cc_final: 0.7688 (mp10)
REVERT: A  173 ASP cc_start: 0.8987 (m-30) cc_final: 0.8521 (p0)
REVERT: A  198 MET cc_start: 0.9168 (tpt) cc_final: 0.8729 (tpt)
REVERT: A  550 ASN cc_start: 0.8146 (OUTLIER) cc_final: 0.7899 (p0)
REVERT: A  564 MET cc_start: 0.7461 (mmp) cc_final: 0.6713 (tpt)
REVERT: B  132 GLN cc_start: 0.8533 (mp10) cc_final: 0.7690 (mp10)
REVERT: B  173 ASP cc_start: 0.8999 (m-30) cc_final: 0.8532 (p0)
REVERT: B  198 MET cc_start: 0.9193 (tpt) cc_final: 0.8743 (tpt)
REVERT: B  550 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7881 (p0)
REVERT: B  564 MET cc_start: 0.7454 (mmp) cc_final: 0.6785 (tpt)
  outliers start: 12
  outliers final: 4
  residues processed: 66
  average time/residue: 1.2594
  time to fit residues: 89.5901
Evaluate side-chains
  63 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  550 ASN
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  550 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 94 optimal weight:    0.0570
   chunk 55 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
B 240 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.074437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.060850 restraints weight = 20731.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 2.69
r_work: 0.2813 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9592  Z= 0.178
  Angle     :  0.461   5.093  12998  Z= 0.247
  Chirality :  0.043   0.149   1426
  Planarity :  0.003   0.025   1668
  Dihedral  :  3.945  15.858   1252
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.90 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1150
  helix:  1.50 (0.27), residues: 396
  sheet: -0.57 (0.43), residues: 138
  loop :  0.27 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 183 
 HIS   0.002   0.001   HIS B 442 
 PHE   0.013   0.001   PHE A 506 
 TYR   0.012   0.001   TYR B 112 
 ARG   0.002   0.000   ARG B  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8586 (mp10) cc_final: 0.7845 (mp10)
REVERT: A  173 ASP cc_start: 0.8954 (m-30) cc_final: 0.8580 (p0)
REVERT: A  506 PHE cc_start: 0.9089 (t80) cc_final: 0.8860 (t80)
REVERT: A  564 MET cc_start: 0.7328 (mmp) cc_final: 0.6425 (tmm)
REVERT: A  582 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7760 (tm-30)
REVERT: B  132 GLN cc_start: 0.8584 (mp10) cc_final: 0.7841 (mp10)
REVERT: B  173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8574 (p0)
REVERT: B  506 PHE cc_start: 0.9089 (t80) cc_final: 0.8862 (t80)
REVERT: B  539 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8429 (mm)
REVERT: B  560 LYS cc_start: 0.8793 (tmmt) cc_final: 0.8582 (ttpp)
REVERT: B  564 MET cc_start: 0.7348 (mmp) cc_final: 0.6481 (tmm)
  outliers start: 18
  outliers final: 8
  residues processed: 75
  average time/residue: 1.3842
  time to fit residues: 111.7538
Evaluate side-chains
  72 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  582 GLU
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 85 optimal weight:    0.7980
   chunk 45 optimal weight:    0.2980
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 83 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.075223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.061898 restraints weight = 20763.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.67
r_work: 0.2831 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9592  Z= 0.161
  Angle     :  0.450   5.417  12998  Z= 0.242
  Chirality :  0.042   0.143   1426
  Planarity :  0.003   0.027   1668
  Dihedral  :  3.802  15.186   1252
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.38 %
    Favored  : 87.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1150
  helix:  1.60 (0.27), residues: 396
  sheet: -0.55 (0.43), residues: 138
  loop :  0.31 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 183 
 HIS   0.002   0.001   HIS B 588 
 PHE   0.012   0.001   PHE B 506 
 TYR   0.010   0.001   TYR B 112 
 ARG   0.006   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8574 (mp10) cc_final: 0.7824 (mp10)
REVERT: A  173 ASP cc_start: 0.8941 (m-30) cc_final: 0.8549 (p0)
REVERT: A  506 PHE cc_start: 0.9032 (t80) cc_final: 0.8773 (t80)
REVERT: A  564 MET cc_start: 0.7317 (mmp) cc_final: 0.6484 (tmm)
REVERT: A  582 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: B   81 ARG cc_start: 0.8208 (mtt90) cc_final: 0.7954 (mtt90)
REVERT: B  132 GLN cc_start: 0.8581 (mp10) cc_final: 0.7847 (mp10)
REVERT: B  173 ASP cc_start: 0.8947 (m-30) cc_final: 0.8552 (p0)
REVERT: B  506 PHE cc_start: 0.9030 (t80) cc_final: 0.8774 (t80)
REVERT: B  564 MET cc_start: 0.7331 (mmp) cc_final: 0.6354 (tmm)
  outliers start: 17
  outliers final: 5
  residues processed: 69
  average time/residue: 1.3905
  time to fit residues: 103.1217
Evaluate side-chains
  66 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  582 GLU
Chi-restraints excluded: chain B residue   28 ILE
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 98 optimal weight:    0.4980
   chunk 51 optimal weight:    0.8980
   chunk 66 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
** A 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 240 HIS
** B 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.075063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.061281 restraints weight = 21212.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.77
r_work: 0.2811 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2816
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.92   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2816 r_free = 0.2816    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2816
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9592  Z= 0.202
  Angle     :  0.468   5.619  12998  Z= 0.252
  Chirality :  0.043   0.140   1426
  Planarity :  0.003   0.032   1668
  Dihedral  :  3.869  14.851   1252
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.58 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1150
  helix:  1.63 (0.27), residues: 396
  sheet: -0.55 (0.44), residues: 138
  loop :  0.35 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 316 
 HIS   0.003   0.001   HIS B 442 
 PHE   0.012   0.001   PHE B 506 
 TYR   0.010   0.001   TYR B 226 
 ARG   0.006   0.000   ARG A  81 

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8579 (mp10) cc_final: 0.7864 (mp10)
REVERT: A  173 ASP cc_start: 0.8957 (m-30) cc_final: 0.8587 (p0)
REVERT: A  506 PHE cc_start: 0.9049 (t80) cc_final: 0.8800 (t80)
REVERT: A  550 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8305 (p0)
REVERT: A  564 MET cc_start: 0.7407 (mmp) cc_final: 0.6398 (tmm)
REVERT: A  582 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7766 (tm-30)
REVERT: B   83 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7880 (mtm)
REVERT: B  132 GLN cc_start: 0.8579 (mp10) cc_final: 0.7861 (mp10)
REVERT: B  173 ASP cc_start: 0.8960 (m-30) cc_final: 0.8587 (p0)
REVERT: B  506 PHE cc_start: 0.9044 (t80) cc_final: 0.8796 (t80)
REVERT: B  550 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8264 (p0)
REVERT: B  564 MET cc_start: 0.7355 (mmp) cc_final: 0.6382 (tmm)
  outliers start: 14
  outliers final: 5
  residues processed: 67
  average time/residue: 1.2062
  time to fit residues: 88.0073
Evaluate side-chains
  67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  550 ASN
Chi-restraints excluded: chain A residue  582 GLU
Chi-restraints excluded: chain B residue   83 MET
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  550 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 60.1387 > 50:
  distance: 47 - 175:  12.424
  distance: 111 - 114:   7.957
  distance: 114 - 115:  17.836
  distance: 115 - 116:  17.889
  distance: 116 - 117:  17.795
  distance: 116 - 118:  22.053
  distance: 118 - 119:  15.549
  distance: 119 - 120:  18.261
  distance: 119 - 122:   7.442
  distance: 120 - 127:  50.887
  distance: 122 - 123:   9.545
  distance: 123 - 124:  12.837
  distance: 124 - 125:  10.283
  distance: 125 - 126:  29.419
  distance: 127 - 128:  11.293
  distance: 128 - 129:  35.847
  distance: 128 - 131:  40.313
  distance: 129 - 130:   9.798
  distance: 129 - 134:   8.992
  distance: 131 - 132:  11.606
  distance: 131 - 133:  33.448
  distance: 134 - 135:  15.661
  distance: 135 - 136:   8.113
  distance: 135 - 138:  40.554
  distance: 136 - 137:   4.131
  distance: 136 - 141:  10.032
  distance: 138 - 139:  12.055
  distance: 138 - 140:  12.028
  distance: 141 - 142:   7.623
  distance: 142 - 145:  11.940
  distance: 143 - 144:   6.181
  distance: 143 - 148:   9.338
  distance: 145 - 146:   6.664
  distance: 145 - 147:  27.880
  distance: 148 - 149:  10.751
  distance: 149 - 150:  12.101
  distance: 150 - 151:  12.633
  distance: 150 - 152:   7.351
  distance: 152 - 153:  15.038
  distance: 153 - 154:   3.532
  distance: 154 - 155:   6.264
  distance: 156 - 157:   4.318
  distance: 158 - 159:   3.444
  distance: 160 - 161:  11.470
  distance: 160 - 162:  12.288
  distance: 161 - 163:   5.047
  distance: 164 - 202:   8.720
  distance: 165 - 168:   5.312
  distance: 166 - 167:   5.744
  distance: 166 - 172:   4.169
  distance: 167 - 199:  11.230
  distance: 168 - 169:   4.736
  distance: 169 - 171:   6.307
  distance: 173 - 174:   5.983
  distance: 174 - 175:   6.703
  distance: 174 - 179:   7.433
  distance: 176 - 177:   5.768
  distance: 176 - 178:  13.948