Starting phenix.real_space_refine
on Fri Oct 10 22:25:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ur3_42480/10_2025/8ur3_42480.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ur3_42480/10_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_42480/10_2025/8ur3_42480.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ur3_42480/10_2025/8ur3_42480.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ur3_42480/10_2025/8ur3_42480.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ur3_42480/10_2025/8ur3_42480.cif"
  }
  resolution = 2.61
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.021
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.34, per 1000 atoms: 0.25
  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: 0.84
  Conformation dependent library (CDL) restraints added in 289.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.37
  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: 1.48

  Time building geometry restraints manager: 1.12 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: 0.02
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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.170
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.010
-------------------------------------------------------------------------------
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= 0.153
  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 : 4.05
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.63 (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
 ARG   0.001   0.000   ARG B  81 
 TYR   0.008   0.001   TYR A 464 
 PHE   0.009   0.001   PHE A  11 
 TRP   0.005   0.001   TRP B 344 
 HIS   0.003   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9592)
  covalent geometry    : angle       0.51295 (12998)
  hydrogen bonds       : bond        0.23843 (  337)
  hydrogen bonds       : angle       7.31285 (  951)

*********************** 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  : 0.405 
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: 0.7778
  time to fit residues: 93.4677
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  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   overall best weight:    2.0988

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

Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A 442 HIS
B 240 HIS
B 442 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.072891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.059798 restraints weight = 21843.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 2.68
r_work: 0.2838 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2691 r_free = 0.2691    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.62   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   9592  Z= 0.281
  Angle     :  0.550   5.160  12998  Z= 0.299
  Chirality :  0.047   0.161   1426
  Planarity :  0.003   0.026   1668
  Dihedral  :  4.309  16.136   1252
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.02 %
    Favored  : 91.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1150
  helix:  0.75 (0.26), residues: 392
  sheet:  0.02 (0.46), residues: 138
  loop :  0.02 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 324 
 TYR   0.012   0.001   TYR A 112 
 PHE   0.018   0.001   PHE A 506 
 TRP   0.005   0.001   TRP A 316 
 HIS   0.002   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 ( 9592)
  covalent geometry    : angle       0.54974 (12998)
  hydrogen bonds       : bond        0.04656 (  337)
  hydrogen bonds       : angle       4.62650 (  951)

*********************** 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
  80 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLU cc_start: 0.8913 (pm20) cc_final: 0.8684 (pm20)
REVERT: A  132 GLN cc_start: 0.8747 (mp10) cc_final: 0.8112 (mp10)
REVERT: A  173 ASP cc_start: 0.9196 (m-30) cc_final: 0.8703 (p0)
REVERT: A  401 ASP cc_start: 0.8831 (m-30) cc_final: 0.8234 (t0)
REVERT: A  564 MET cc_start: 0.7534 (mmp) cc_final: 0.6741 (tpt)
REVERT: B   18 GLU cc_start: 0.8915 (pm20) cc_final: 0.8689 (pm20)
REVERT: B  132 GLN cc_start: 0.8758 (mp10) cc_final: 0.8128 (mp10)
REVERT: B  173 ASP cc_start: 0.9187 (m-30) cc_final: 0.8701 (p0)
REVERT: B  401 ASP cc_start: 0.8818 (m-30) cc_final: 0.8219 (t0)
REVERT: B  564 MET cc_start: 0.7485 (mmp) cc_final: 0.6732 (tpt)
REVERT: B  574 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8582 (pptt)
  outliers start: 12
  outliers final: 4
  residues processed: 74
  average time/residue: 0.6756
  time to fit residues: 53.2692
Evaluate side-chains
  67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  574 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.074602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.061146 restraints weight = 21001.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 2.71
r_work: 0.2809 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2809
-------------------------------------------------------------------------------
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 = 0.81   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 = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9592  Z= 0.142
  Angle     :  0.465   4.920  12998  Z= 0.249
  Chirality :  0.043   0.154   1426
  Planarity :  0.003   0.024   1668
  Dihedral  :  4.012  16.050   1252
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.13 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.25), residues: 1150
  helix:  1.20 (0.27), residues: 394
  sheet: -0.27 (0.44), residues: 138
  loop :  0.20 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.012   0.001   TYR A 112 
 PHE   0.011   0.001   PHE A 506 
 TRP   0.005   0.001   TRP B 192 
 HIS   0.002   0.001   HIS B 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9592)
  covalent geometry    : angle       0.46483 (12998)
  hydrogen bonds       : bond        0.03605 (  337)
  hydrogen bonds       : angle       4.28680 (  951)

*********************** 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
  73 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8557 (mp10) cc_final: 0.7809 (mp10)
REVERT: A  173 ASP cc_start: 0.8964 (m-30) cc_final: 0.8579 (p0)
REVERT: A  506 PHE cc_start: 0.9034 (t80) cc_final: 0.8760 (t80)
REVERT: A  564 MET cc_start: 0.7411 (mmp) cc_final: 0.6649 (tpt)
REVERT: B  132 GLN cc_start: 0.8565 (mp10) cc_final: 0.7846 (mp10)
REVERT: B  173 ASP cc_start: 0.8949 (m-30) cc_final: 0.8575 (p0)
REVERT: B  506 PHE cc_start: 0.9023 (t80) cc_final: 0.8749 (t80)
REVERT: B  564 MET cc_start: 0.7371 (mmp) cc_final: 0.6712 (tpt)
  outliers start: 10
  outliers final: 6
  residues processed: 65
  average time/residue: 0.5898
  time to fit residues: 41.4884
Evaluate side-chains
  65 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  529 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    0.0970
   chunk 68 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 23 optimal weight:    0.8980
   chunk 112 optimal weight:    8.9990
   chunk 35 optimal weight:    9.9990
   chunk 88 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 95 optimal weight:    7.9990
   overall best weight:    1.7782

-------------------------------------------------------------------------------
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 = 0.3227 r_free = 0.3227 target = 0.072662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.059206 restraints weight = 21079.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.66
r_work: 0.2770 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2615 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2617
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2617 r_free = 0.2617    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2617
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8609
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9592  Z= 0.239
  Angle     :  0.506   5.027  12998  Z= 0.273
  Chirality :  0.045   0.146   1426
  Planarity :  0.003   0.026   1668
  Dihedral  :  4.133  15.935   1252
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.33 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.25), residues: 1150
  helix:  1.43 (0.27), residues: 394
  sheet: -0.46 (0.44), residues: 138
  loop :  0.21 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  81 
 TYR   0.011   0.001   TYR A 226 
 PHE   0.013   0.001   PHE A 506 
 TRP   0.006   0.001   TRP A 316 
 HIS   0.004   0.001   HIS B 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 9592)
  covalent geometry    : angle       0.50635 (12998)
  hydrogen bonds       : bond        0.03725 (  337)
  hydrogen bonds       : angle       4.20832 (  951)

*********************** 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
  74 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8691 (mp10) cc_final: 0.7858 (mp10)
REVERT: A  173 ASP cc_start: 0.9163 (m-30) cc_final: 0.8655 (p0)
REVERT: A  564 MET cc_start: 0.7520 (mmp) cc_final: 0.6585 (tmm)
REVERT: B  132 GLN cc_start: 0.8678 (mp10) cc_final: 0.7846 (mp10)
REVERT: B  173 ASP cc_start: 0.9172 (m-30) cc_final: 0.8665 (p0)
REVERT: B  539 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8334 (mm)
REVERT: B  564 MET cc_start: 0.7480 (mmp) cc_final: 0.6729 (tpt)
  outliers start: 18
  outliers final: 6
  residues processed: 66
  average time/residue: 0.6291
  time to fit residues: 44.6340
Evaluate side-chains
  63 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  529 ILE
Chi-restraints excluded: chain B residue  539 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    0.5980
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0470
   chunk 22 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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
B 550 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.075165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.061753 restraints weight = 20938.799|
|-----------------------------------------------------------------------------|
r_work (start): 0.2984 rms_B_bonded: 2.69
r_work: 0.2827 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9592  Z= 0.105
  Angle     :  0.447   5.207  12998  Z= 0.240
  Chirality :  0.042   0.147   1426
  Planarity :  0.003   0.026   1668
  Dihedral  :  3.839  15.892   1252
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  :  9.52 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1150
  helix:  1.56 (0.27), residues: 396
  sheet: -0.54 (0.43), residues: 138
  loop :  0.28 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.012   0.001   TYR A 112 
 PHE   0.007   0.001   PHE A 506 
 TRP   0.006   0.001   TRP B 183 
 HIS   0.001   0.000   HIS B 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9592)
  covalent geometry    : angle       0.44670 (12998)
  hydrogen bonds       : bond        0.02999 (  337)
  hydrogen bonds       : angle       4.04794 (  951)

*********************** 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
  86 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8578 (mp10) cc_final: 0.7846 (mp10)
REVERT: A  173 ASP cc_start: 0.8971 (m-30) cc_final: 0.8569 (p0)
REVERT: A  506 PHE cc_start: 0.9025 (t80) cc_final: 0.8768 (t80)
REVERT: A  550 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8251 (p0)
REVERT: A  564 MET cc_start: 0.7314 (mmp) cc_final: 0.6402 (tmm)
REVERT: B  132 GLN cc_start: 0.8569 (mp10) cc_final: 0.7831 (mp10)
REVERT: B  173 ASP cc_start: 0.8965 (m-30) cc_final: 0.8568 (p0)
REVERT: B  506 PHE cc_start: 0.9020 (t80) cc_final: 0.8761 (t80)
REVERT: B  550 ASN cc_start: 0.8463 (OUTLIER) cc_final: 0.8259 (p0)
REVERT: B  564 MET cc_start: 0.7330 (mmp) cc_final: 0.6457 (tmm)
  outliers start: 21
  outliers final: 2
  residues processed: 76
  average time/residue: 0.6359
  time to fit residues: 51.8615
Evaluate side-chains
  62 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  550 ASN
Chi-restraints excluded: chain B residue  508 THR
Chi-restraints excluded: chain B residue  550 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 79 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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
B 550 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.074197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.060625 restraints weight = 21020.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.2961 rms_B_bonded: 2.69
r_work: 0.2801 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.2801
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2324

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= 0.158
  Angle     :  0.464   5.237  12998  Z= 0.249
  Chirality :  0.043   0.141   1426
  Planarity :  0.003   0.028   1668
  Dihedral  :  3.913  15.633   1252
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.48 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.25), residues: 1150
  helix:  1.65 (0.27), residues: 396
  sheet: -0.57 (0.43), residues: 138
  loop :  0.29 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.009   0.001   TYR B 112 
 PHE   0.009   0.001   PHE A 506 
 TRP   0.006   0.001   TRP B 316 
 HIS   0.003   0.001   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9592)
  covalent geometry    : angle       0.46389 (12998)
  hydrogen bonds       : bond        0.03188 (  337)
  hydrogen bonds       : angle       4.04860 (  951)

*********************** 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
  76 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8570 (mp10) cc_final: 0.7784 (mp10)
REVERT: A  173 ASP cc_start: 0.8971 (m-30) cc_final: 0.8579 (p0)
REVERT: A  506 PHE cc_start: 0.9048 (t80) cc_final: 0.8806 (t80)
REVERT: A  550 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8443 (p0)
REVERT: A  564 MET cc_start: 0.7354 (mmp) cc_final: 0.6516 (tmm)
REVERT: B  132 GLN cc_start: 0.8572 (mp10) cc_final: 0.7785 (mp10)
REVERT: B  173 ASP cc_start: 0.8966 (m-30) cc_final: 0.8576 (p0)
REVERT: B  506 PHE cc_start: 0.9041 (t80) cc_final: 0.8797 (t80)
REVERT: B  539 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8256 (mm)
REVERT: B  550 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8447 (p0)
REVERT: B  564 MET cc_start: 0.7371 (mmp) cc_final: 0.6396 (tmm)
  outliers start: 16
  outliers final: 2
  residues processed: 70
  average time/residue: 0.6827
  time to fit residues: 51.1560
Evaluate side-chains
  63 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  550 ASN
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0370
   chunk 97 optimal weight:    3.9990
   chunk 87 optimal weight:    0.4980
   chunk 59 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0060
   chunk 64 optimal weight:    0.4980
   chunk 50 optimal weight:    0.9980
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.3874

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

Flipped N/Q/H residues before XYZ refinement:
A 550 ASN
B 550 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.076563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.062747 restraints weight = 21186.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 2.72
r_work: 0.2845 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2847 r_free = 0.2847    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2846 r_free = 0.2846    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.93   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2846
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9592  Z= 0.095
  Angle     :  0.457   5.653  12998  Z= 0.244
  Chirality :  0.042   0.142   1426
  Planarity :  0.003   0.028   1668
  Dihedral  :  3.755  15.388   1252
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.26), residues: 1150
  helix:  1.72 (0.27), residues: 396
  sheet: -0.57 (0.43), residues: 138
  loop :  0.34 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.011   0.001   TYR B 112 
 PHE   0.005   0.001   PHE A 506 
 TRP   0.007   0.001   TRP B 183 
 HIS   0.001   0.000   HIS A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 9592)
  covalent geometry    : angle       0.45687 (12998)
  hydrogen bonds       : bond        0.02815 (  337)
  hydrogen bonds       : angle       3.98069 (  951)

*********************** 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
  78 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 1.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8546 (mp10) cc_final: 0.7757 (mp10)
REVERT: A  173 ASP cc_start: 0.8973 (m-30) cc_final: 0.8566 (p0)
REVERT: A  506 PHE cc_start: 0.9001 (t80) cc_final: 0.8760 (t80)
REVERT: A  550 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8388 (p0)
REVERT: A  564 MET cc_start: 0.7307 (mmp) cc_final: 0.6452 (tmm)
REVERT: B  132 GLN cc_start: 0.8550 (mp10) cc_final: 0.7760 (mp10)
REVERT: B  173 ASP cc_start: 0.8963 (m-30) cc_final: 0.8563 (p0)
REVERT: B  506 PHE cc_start: 0.8998 (t80) cc_final: 0.8754 (t80)
REVERT: B  550 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8364 (p0)
REVERT: B  564 MET cc_start: 0.7292 (mmp) cc_final: 0.6314 (tmm)
  outliers start: 16
  outliers final: 6
  residues processed: 68
  average time/residue: 0.6059
  time to fit residues: 44.4437
Evaluate side-chains
  70 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  508 THR
Chi-restraints excluded: chain A residue  550 ASN
Chi-restraints excluded: chain B residue    1 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  550 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   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 550 ASN
B 550 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.075807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.062011 restraints weight = 21217.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.71
r_work: 0.2831 rms_B_bonded: 3.07 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 = 0.93   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 = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2493

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= 0.120
  Angle     :  0.460   7.576  12998  Z= 0.245
  Chirality :  0.043   0.138   1426
  Planarity :  0.003   0.031   1668
  Dihedral  :  3.752  15.165   1252
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.96 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1150
  helix:  1.74 (0.27), residues: 396
  sheet: -0.52 (0.43), residues: 138
  loop :  0.36 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.009   0.001   TYR B 112 
 PHE   0.007   0.001   PHE B 506 
 TRP   0.006   0.001   TRP A 316 
 HIS   0.002   0.001   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9592)
  covalent geometry    : angle       0.46006 (12998)
  hydrogen bonds       : bond        0.02928 (  337)
  hydrogen bonds       : angle       3.96880 (  951)

*********************** REFINEMENT MACRO_CYCLE 8 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: 12
    poor density    : 62
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8568 (mp10) cc_final: 0.7855 (mp10)
REVERT: A  173 ASP cc_start: 0.8962 (m-30) cc_final: 0.8584 (p0)
REVERT: A  506 PHE cc_start: 0.9008 (t80) cc_final: 0.8773 (t80)
REVERT: A  564 MET cc_start: 0.7318 (mmp) cc_final: 0.6364 (tmm)
REVERT: B  132 GLN cc_start: 0.8573 (mp10) cc_final: 0.7859 (mp10)
REVERT: B  173 ASP cc_start: 0.8956 (m-30) cc_final: 0.8583 (p0)
REVERT: B  506 PHE cc_start: 0.9004 (t80) cc_final: 0.8767 (t80)
REVERT: B  564 MET cc_start: 0.7312 (mmp) cc_final: 0.6348 (tmm)
  outliers start: 12
  outliers final: 3
  residues processed: 68
  average time/residue: 0.5915
  time to fit residues: 43.4569
Evaluate side-chains
  61 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.5188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.073527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.059842 restraints weight = 20981.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.69
r_work: 0.2783 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.91   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9592  Z= 0.207
  Angle     :  0.510   7.078  12998  Z= 0.273
  Chirality :  0.045   0.139   1426
  Planarity :  0.003   0.030   1668
  Dihedral  :  4.023  15.319   1252
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  : 11.44 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1150
  helix:  1.65 (0.27), residues: 398
  sheet: -0.58 (0.43), residues: 138
  loop :  0.35 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.009   0.001   TYR A 226 
 PHE   0.011   0.001   PHE B 506 
 TRP   0.006   0.001   TRP B 316 
 HIS   0.004   0.001   HIS B 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 9592)
  covalent geometry    : angle       0.51010 (12998)
  hydrogen bonds       : bond        0.03391 (  337)
  hydrogen bonds       : angle       4.08491 (  951)

*********************** REFINEMENT MACRO_CYCLE 9 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
  68 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8535 (mp10) cc_final: 0.7752 (mp10)
REVERT: A  173 ASP cc_start: 0.8984 (m-30) cc_final: 0.8611 (p0)
REVERT: A  564 MET cc_start: 0.7408 (mmp) cc_final: 0.6413 (tmm)
REVERT: B  132 GLN cc_start: 0.8535 (mp10) cc_final: 0.7753 (mp10)
REVERT: B  173 ASP cc_start: 0.8980 (m-30) cc_final: 0.8605 (p0)
REVERT: B  560 LYS cc_start: 0.8807 (pttm) cc_final: 0.8588 (ttpp)
REVERT: B  564 MET cc_start: 0.7401 (mmp) cc_final: 0.6416 (tmm)
  outliers start: 8
  outliers final: 6
  residues processed: 62
  average time/residue: 0.6444
  time to fit residues: 42.9608
Evaluate side-chains
  65 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
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 B residue  389 MET
Chi-restraints excluded: chain B residue  392 THR
Chi-restraints excluded: chain B residue  465 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 90 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0470
   chunk 38 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.5678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.075844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.062029 restraints weight = 21077.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.73
r_work: 0.2829 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9592  Z= 0.105
  Angle     :  0.467   7.550  12998  Z= 0.248
  Chirality :  0.043   0.141   1426
  Planarity :  0.003   0.031   1668
  Dihedral  :  3.835  14.894   1252
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 11.92 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.26), residues: 1150
  helix:  1.75 (0.27), residues: 396
  sheet: -0.54 (0.43), residues: 138
  loop :  0.38 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.011   0.001   TYR B 112 
 PHE   0.006   0.001   PHE A  94 
 TRP   0.006   0.001   TRP B 183 
 HIS   0.001   0.000   HIS B 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 9592)
  covalent geometry    : angle       0.46749 (12998)
  hydrogen bonds       : bond        0.02885 (  337)
  hydrogen bonds       : angle       3.96254 (  951)

********************** REFINEMENT MACRO_CYCLE 10 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
  67 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.8574 (mp10) cc_final: 0.7847 (mp10)
REVERT: A  173 ASP cc_start: 0.8962 (m-30) cc_final: 0.8603 (p0)
REVERT: A  506 PHE cc_start: 0.9046 (t80) cc_final: 0.8807 (t80)
REVERT: A  564 MET cc_start: 0.7397 (mmp) cc_final: 0.6371 (tmm)
REVERT: B  132 GLN cc_start: 0.8576 (mp10) cc_final: 0.7846 (mp10)
REVERT: B  173 ASP cc_start: 0.8949 (m-30) cc_final: 0.8594 (p0)
REVERT: B  506 PHE cc_start: 0.9046 (t80) cc_final: 0.8807 (t80)
REVERT: B  564 MET cc_start: 0.7332 (mmp) cc_final: 0.6323 (tmm)
  outliers start: 6
  outliers final: 3
  residues processed: 61
  average time/residue: 0.6327
  time to fit residues: 41.5792
Evaluate side-chains
  64 residues out of total 1040 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  392 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain B residue  392 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   chunk 78 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 63 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   overall best weight:    2.3988

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.072176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.058559 restraints weight = 20982.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.67
r_work: 0.2752 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2598 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2599
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2599 r_free = 0.2599    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2599
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   9592  Z= 0.310
  Angle     :  0.560   6.706  12998  Z= 0.300
  Chirality :  0.047   0.139   1426
  Planarity :  0.003   0.030   1668
  Dihedral  :  4.228  15.383   1252
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 12.21 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.25), residues: 1150
  helix:  1.64 (0.27), residues: 396
  sheet: -0.57 (0.43), residues: 138
  loop :  0.33 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  81 
 TYR   0.014   0.001   TYR A 226 
 PHE   0.014   0.001   PHE A 506 
 TRP   0.007   0.001   TRP B 344 
 HIS   0.006   0.001   HIS A 442 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 ( 9592)
  covalent geometry    : angle       0.55961 (12998)
  hydrogen bonds       : bond        0.03728 (  337)
  hydrogen bonds       : angle       4.13921 (  951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3002.23 seconds
wall clock time: 52 minutes 7.42 seconds (3127.42 seconds total)