Starting phenix.real_space_refine
on Wed Mar  4 00:07:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2026/7bcw_12145.map"
  }
  resolution = 3.5
  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=   0.003 sd=   0.041
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: 7
    Type Number    sf(0)   Gaussians
     V       2      8.30       5
     P       6      5.49       5
     Mg      2      5.21       5
     S      54      5.16       5
     C    5696      2.51       5
     N    1560      2.21       5
     O    1705      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9025
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4452
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 13, 'TRANS': 560}
    Chain: "B"
      Number of atoms: 4452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4452
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 13, 'TRANS': 560}
    Chain: "A"
      Number of atoms: 65
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 65
          Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'POV:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {' MG': 1, 'ADP': 1, 'POV': 1, 'VO4': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'POV:plan-3': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 2.23, per 1000 atoms: 0.25
  Number of scatterers: 9025
  At special positions: 0
  Unit cell: (77.738, 79.392, 141.417, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     V       2     22.97
     S      54     16.00
     P       6     15.00
     Mg      2     11.99
     O    1705      8.00
     N    1560      7.00
     C    5696      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: 0.59
  Conformation dependent library (CDL) restraints added in 274.5 milliseconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2148

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 5 sheets defined
      67.3% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 24 through 46
      removed outlier: 4.212A  pdb=" N   VAL A  29 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A  30 " --> pdb=" O   GLY A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 54
    Processing helix  chain 'A' and resid 66 through 109
      removed outlier: 3.869A  pdb=" N   VAL A  70 " --> pdb=" O   TRP A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
    Processing helix  chain 'A' and resid 120 through 130
      removed outlier: 3.845A  pdb=" N   LEU A 124 " --> pdb=" O   SER A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 141
    Processing helix  chain 'A' and resid 141 through 164
      removed outlier: 3.741A  pdb=" N   THR A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 213
      removed outlier: 3.787A  pdb=" N   VAL A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.759A  pdb=" N   ARG A 188 " --> pdb=" O   VAL A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
    Processing helix  chain 'A' and resid 222 through 271
      removed outlier: 3.604A  pdb=" N   GLU A 226 " --> pdb=" O   GLY A 222 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.557A  pdb=" N   LEU A 261 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   LEU A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.696A  pdb=" N   ASP A 277 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 323
      removed outlier: 3.796A  pdb=" N   MET A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.552A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   GLN A 307 " --> pdb=" O   ASN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 389
      removed outlier: 3.729A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 417
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 464
      removed outlier: 3.541A  pdb=" N   ASN A 464 " --> pdb=" O   MET A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
    Processing helix  chain 'A' and resid 482 through 487
    Processing helix  chain 'A' and resid 488 through 497
      removed outlier: 3.531A  pdb=" N   ALA A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ARG A 497 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 527
    Processing helix  chain 'A' and resid 561 through 567
    Processing helix  chain 'A' and resid 570 through 577
    Processing helix  chain 'B' and resid 8 through 21
      Proline residue:  B  18  - end of helix
    Processing helix  chain 'B' and resid 24 through 47
      removed outlier: 3.659A  pdb=" N   LEU B  45 " --> pdb=" O   ASP B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 54
    Processing helix  chain 'B' and resid 58 through 62
    Processing helix  chain 'B' and resid 66 through 109
      removed outlier: 4.070A  pdb=" N   VAL B  92 " --> pdb=" O   CYS B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
    Processing helix  chain 'B' and resid 120 through 141
      removed outlier: 3.825A  pdb=" N   LEU B 124 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 164
      removed outlier: 3.732A  pdb=" N   THR B 145 " --> pdb=" O   GLY B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 212
      removed outlier: 3.661A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 4.223A  pdb=" N   ARG B 188 " --> pdb=" O   VAL B 184 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ASN B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
      removed outlier: 3.599A  pdb=" N   PHE B 220 " --> pdb=" O   GLU B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 271
      Proline residue:  B 253  - end of helix
      removed outlier: 4.138A  pdb=" N   ALA B 262 " --> pdb=" O   ILE B 258 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU B 263 " --> pdb=" O   ALA B 259 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 323
      Proline residue:  B 297  - end of helix
      removed outlier: 4.692A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 5.146A  pdb=" N   GLN B 307 " --> pdb=" O   ASN B 303 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASP B 323 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 391
    Processing helix  chain 'B' and resid 415 through 417
      No H-bonds generated for 'chain 'B' and resid 415 through 417'
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.624A  pdb=" N   THR B 472 " --> pdb=" O   GLY B 469 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 479
    Processing helix  chain 'B' and resid 482 through 497
      removed outlier: 4.052A  pdb=" N   ARG B 497 " --> pdb=" O   ARG B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 524
    Processing helix  chain 'B' and resid 525 through 529
      removed outlier: 3.751A  pdb=" N   LYS B 528 " --> pdb=" O   GLU B 525 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 569
    Processing helix  chain 'B' and resid 570 through 578
      removed outlier: 3.512A  pdb=" N   GLN B 574 " --> pdb=" O   GLY B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 365 through 366
      removed outlier: 4.483A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 7.115A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.362A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   ASP A 505 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   VAL A 422 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 7.510A  pdb=" N   ILE A 535 " --> pdb=" O   LEU A 502 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   LEU A 504 " --> pdb=" O   ILE A 535 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU A 558 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   GLU A 552 " --> pdb=" O   ILE A 556 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   ILE A 556 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 359 through 362
      removed outlier: 5.990A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 359 through 362
      removed outlier: 5.990A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   VAL B 347 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   GLU B 397 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.598A  pdb=" N   ALA B 420 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   ASP B 505 " --> pdb=" O   ALA B 420 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL B 422 " --> pdb=" O   ASP B 505 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   VAL B 375 " --> pdb=" O   VAL B 551 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU B 558 " --> pdb=" O   VAL B 550 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1626 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: 1.16

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.18 -     1.33: 1877
        1.33 -     1.47: 3147
        1.47 -     1.62: 4013
        1.62 -     1.76: 5
        1.76 -     1.91: 111
  Bond restraints: 9153
  Sorted by residual:
  bond pdb=" C21 POV A 604 "
       pdb=" O21 POV A 604 "
    ideal  model  delta    sigma   weight residual
    1.330  1.404 -0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C21 POV B 604 "
       pdb=" O21 POV B 604 "
    ideal  model  delta    sigma   weight residual
    1.330  1.404 -0.074 2.00e-02 2.50e+03 1.35e+01
  bond pdb=" C31 POV A 604 "
       pdb=" O31 POV A 604 "
    ideal  model  delta    sigma   weight residual
    1.327  1.398 -0.071 2.00e-02 2.50e+03 1.26e+01
  bond pdb=" CB  MET A 242 "
       pdb=" CG  MET A 242 "
    ideal  model  delta    sigma   weight residual
    1.520  1.469  0.051 3.00e-02 1.11e+03 2.89e+00
  bond pdb=" C28 POV B 604 "
       pdb=" C29 POV B 604 "
    ideal  model  delta    sigma   weight residual
    1.497  1.528 -0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 9148 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 12182
        2.50 -     5.01: 152
        5.01 -     7.51: 31
        7.51 -    10.02: 5
       10.02 -    12.52: 4
  Bond angle restraints: 12374
  Sorted by residual:
  angle pdb=" O13 POV A 604 "
        pdb=" P   POV A 604 "
        pdb=" O14 POV A 604 "
      ideal   model   delta    sigma   weight residual
     121.11  108.59   12.52 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" O11 POV A 604 "
        pdb=" P   POV A 604 "
        pdb=" O12 POV A 604 "
      ideal   model   delta    sigma   weight residual
      97.67  109.98  -12.31 3.00e+00 1.11e-01 1.68e+01
  angle pdb=" O13 POV B 604 "
        pdb=" P   POV B 604 "
        pdb=" O14 POV B 604 "
      ideal   model   delta    sigma   weight residual
     121.11  109.01   12.10 3.00e+00 1.11e-01 1.63e+01
  angle pdb=" O11 POV B 604 "
        pdb=" P   POV B 604 "
        pdb=" O12 POV B 604 "
      ideal   model   delta    sigma   weight residual
      97.67  109.66  -11.99 3.00e+00 1.11e-01 1.60e+01
  angle pdb=" CB  MET B 276 "
        pdb=" CG  MET B 276 "
        pdb=" SD  MET B 276 "
      ideal   model   delta    sigma   weight residual
     112.70  122.24   -9.54 3.00e+00 1.11e-01 1.01e+01
  ... (remaining 12369 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.75: 5373
       30.75 -    61.50: 171
       61.50 -    92.25: 19
       92.25 -   123.00: 0
      123.00 -   153.75: 5
  Dihedral angle restraints: 5568
    sinusoidal: 2248
      harmonic: 3320
  Sorted by residual:
  dihedral pdb=" O2A ADP B 602 "
           pdb=" O3A ADP B 602 "
           pdb=" PA  ADP B 602 "
           pdb=" PB  ADP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   73.70 -133.70     1      2.00e+01 2.50e-03 4.06e+01
  dihedral pdb=" O1B ADP B 602 "
           pdb=" O3A ADP B 602 "
           pdb=" PB  ADP B 602 "
           pdb=" PA  ADP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   73.08 -133.08     1      2.00e+01 2.50e-03 4.04e+01
  dihedral pdb=" O1B ADP A 602 "
           pdb=" O3A ADP A 602 "
           pdb=" PB  ADP A 602 "
           pdb=" PA  ADP A 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  172.88  127.11     1      2.00e+01 2.50e-03 3.85e+01
  ... (remaining 5565 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 756
       0.029 -    0.058: 460
       0.058 -    0.087: 167
       0.087 -    0.116: 67
       0.116 -    0.144: 16
  Chirality restraints: 1466
  Sorted by residual:
  chirality pdb=" CA  ILE B 400 "
            pdb=" N   ILE B 400 "
            pdb=" C   ILE B 400 "
            pdb=" CB  ILE B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.21e-01
  chirality pdb=" CA  VAL A 342 "
            pdb=" N   VAL A 342 "
            pdb=" C   VAL A 342 "
            pdb=" CB  VAL A 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.94e-01
  chirality pdb=" CA  ILE B 535 "
            pdb=" N   ILE B 535 "
            pdb=" C   ILE B 535 "
            pdb=" CB  ILE B 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  ... (remaining 1463 not shown)

  Planarity restraints: 1552
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  67 "   -0.031 5.00e-02 4.00e+02   4.66e-02 3.48e+00
        pdb=" N   PRO A  68 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 542 "   -0.008 2.00e-02 2.50e+03   1.47e-02 2.15e+00
        pdb=" C   ILE A 542 "    0.025 2.00e-02 2.50e+03
        pdb=" O   ILE A 542 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLU A 543 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 175 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO B 176 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 176 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 176 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1549 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 43
        2.47 -     3.08: 6634
        3.08 -     3.69: 13610
        3.69 -     4.29: 19418
        4.29 -     4.90: 32740
  Nonbonded interactions: 72445
  Sorted by model distance:
  nonbonded pdb=" O2  VO4 B 601 "
            pdb="MG    MG B 603 "
     model   vdw
     1.868 2.170
  nonbonded pdb=" OG  SER B 383 "
            pdb="MG    MG B 603 "
     model   vdw
     1.889 2.170
  nonbonded pdb=" OE1 GLN B 424 "
            pdb="MG    MG B 603 "
     model   vdw
     1.942 2.170
  nonbonded pdb=" O1B ADP B 602 "
            pdb="MG    MG B 603 "
     model   vdw
     1.969 2.170
  nonbonded pdb=" OE1 GLN A 424 "
            pdb="MG    MG A 603 "
     model   vdw
     2.018 2.170
  ... (remaining 72440 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 603 or (resid 604 and (name C1 or name C2 or nam \ 
e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ 
 name C28 or name C29 or name C3 or name O11 or name O12 or name O13 or name O14 \ 
 or name O21 or name O22 or name O31))))
  selection = (chain 'B' and (resid 6 through 603 or (resid 604 and (name C1 or name C2 or nam \ 
e C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or \ 
 name C28 or name C29 or name C3 or name O11 or name O12 or name O13 or name O14 \ 
 or name O21 or name O22 or name O31))))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.200
  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:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.840
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
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      :  0.005   0.074   9153  Z= 0.234
  Angle     :  0.760  12.522  12374  Z= 0.373
  Chirality :  0.043   0.144   1466
  Planarity :  0.003   0.047   1552
  Dihedral  : 15.867 153.755   3420
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.25), residues: 1144
  helix:  1.18 (0.20), residues: 714
  sheet: -0.10 (0.60), residues: 68
  loop : -1.14 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 377 
 TYR   0.007   0.001   TYR A  83 
 PHE   0.014   0.001   PHE A  56 
 TRP   0.010   0.002   TRP B  91 
 HIS   0.011   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 9153)
  covalent geometry    : angle       0.75976 (12374)
  hydrogen bonds       : bond        0.15808 (  552)
  hydrogen bonds       : angle       5.86845 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  158 ILE cc_start: 0.8858 (pt) cc_final: 0.8652 (mt)
REVERT: B  403 ASP cc_start: 0.7550 (t0) cc_final: 0.7211 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0882
  time to fit residues: 14.2988
Evaluate side-chains
  93 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    0.7980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
B 435 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.119251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.106407 restraints weight = 15274.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.109496 restraints weight = 6706.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.111433 restraints weight = 3719.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.112655 restraints weight = 2448.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113333 restraints weight = 1827.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9153  Z= 0.123
  Angle     :  0.580   8.521  12374  Z= 0.286
  Chirality :  0.040   0.144   1466
  Planarity :  0.003   0.035   1552
  Dihedral  : 10.294 155.916   1314
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.26 %
    Favored  : 91.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.25), residues: 1144
  helix:  1.60 (0.20), residues: 728
  sheet: -0.04 (0.62), residues: 70
  loop : -1.17 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 391 
 TYR   0.010   0.001   TYR A 572 
 PHE   0.023   0.001   PHE A  43 
 TRP   0.010   0.001   TRP B 165 
 HIS   0.008   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 9153)
  covalent geometry    : angle       0.58049 (12374)
  hydrogen bonds       : bond        0.04733 (  552)
  hydrogen bonds       : angle       4.20909 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8218 (tm-30)
REVERT: A  210 MET cc_start: 0.8724 (tmm) cc_final: 0.8481 (tmm)
REVERT: A  212 LYS cc_start: 0.7872 (tttm) cc_final: 0.7440 (ttpt)
REVERT: B  242 MET cc_start: 0.8382 (mmm) cc_final: 0.8161 (mmm)
REVERT: B  403 ASP cc_start: 0.7691 (t0) cc_final: 0.7264 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 123
  average time/residue: 0.0799
  time to fit residues: 14.3197
Evaluate side-chains
  104 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain B residue  245 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0030
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0470
   chunk 9 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 113 optimal weight:    6.9990
   overall best weight:    0.4688

-------------------------------------------------------------------------------
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 = 0.3595 r_free = 0.3595 target = 0.118695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.106210 restraints weight = 15113.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109265 restraints weight = 6505.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111154 restraints weight = 3571.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.112189 restraints weight = 2335.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113046 restraints weight = 1785.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9153  Z= 0.110
  Angle     :  0.558  10.817  12374  Z= 0.270
  Chirality :  0.040   0.150   1466
  Planarity :  0.003   0.030   1552
  Dihedral  :  9.899 147.126   1314
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.45 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.26), residues: 1144
  helix:  1.87 (0.20), residues: 728
  sheet:  0.04 (0.61), residues: 70
  loop : -1.00 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 377 
 TYR   0.008   0.001   TYR A 572 
 PHE   0.010   0.001   PHE B  56 
 TRP   0.007   0.001   TRP B 165 
 HIS   0.009   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 9153)
  covalent geometry    : angle       0.55772 (12374)
  hydrogen bonds       : bond        0.04144 (  552)
  hydrogen bonds       : angle       3.85264 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8267 (tm-30)
REVERT: A  212 LYS cc_start: 0.7800 (tttm) cc_final: 0.7460 (ttpt)
REVERT: B  210 MET cc_start: 0.9202 (tmm) cc_final: 0.8952 (tmm)
REVERT: B  403 ASP cc_start: 0.7678 (t0) cc_final: 0.7311 (t0)
REVERT: B  427 HIS cc_start: 0.6909 (t-90) cc_final: 0.6470 (t-90)
  outliers start: 13
  outliers final: 8
  residues processed: 121
  average time/residue: 0.0851
  time to fit residues: 14.6776
Evaluate side-chains
  111 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 85 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B 305 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.118940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.105894 restraints weight = 15526.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.109009 restraints weight = 6738.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.110966 restraints weight = 3740.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112195 restraints weight = 2459.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.112878 restraints weight = 1841.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9153  Z= 0.124
  Angle     :  0.554   9.534  12374  Z= 0.267
  Chirality :  0.040   0.143   1466
  Planarity :  0.003   0.030   1552
  Dihedral  :  9.650 136.848   1314
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 11.76 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.26), residues: 1144
  helix:  1.98 (0.20), residues: 730
  sheet: -0.00 (0.61), residues: 70
  loop : -1.02 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.008   0.001   TYR A 572 
 PHE   0.020   0.001   PHE B 265 
 TRP   0.006   0.001   TRP B 165 
 HIS   0.009   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9153)
  covalent geometry    : angle       0.55414 (12374)
  hydrogen bonds       : bond        0.04072 (  552)
  hydrogen bonds       : angle       3.77824 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A  196 MET cc_start: 0.7826 (ttt) cc_final: 0.7337 (ttt)
REVERT: A  208 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: A  212 LYS cc_start: 0.7800 (tttm) cc_final: 0.6930 (mtpt)
REVERT: B  159 MET cc_start: 0.8617 (tmm) cc_final: 0.8407 (tmm)
REVERT: B  242 MET cc_start: 0.8426 (mmp) cc_final: 0.8179 (mmm)
REVERT: B  403 ASP cc_start: 0.7691 (t0) cc_final: 0.7313 (t0)
REVERT: B  427 HIS cc_start: 0.7035 (t-90) cc_final: 0.6834 (t70)
  outliers start: 23
  outliers final: 15
  residues processed: 126
  average time/residue: 0.0790
  time to fit residues: 14.6386
Evaluate side-chains
  123 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  466 MET
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 105 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0980
   chunk 49 optimal weight:    5.9990
   chunk 95 optimal weight:    0.5980
   chunk 50 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.118891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.105735 restraints weight = 15371.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.108853 restraints weight = 6772.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.110811 restraints weight = 3768.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.111983 restraints weight = 2496.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.112785 restraints weight = 1901.276|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9153  Z= 0.123
  Angle     :  0.556   8.394  12374  Z= 0.268
  Chirality :  0.040   0.143   1466
  Planarity :  0.003   0.030   1552
  Dihedral  :  9.310 127.245   1314
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 12.07 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.26), residues: 1144
  helix:  2.03 (0.20), residues: 730
  sheet: -0.05 (0.60), residues: 70
  loop : -0.93 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.008   0.001   TYR A 572 
 PHE   0.014   0.001   PHE B 265 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.009   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 9153)
  covalent geometry    : angle       0.55558 (12374)
  hydrogen bonds       : bond        0.04045 (  552)
  hydrogen bonds       : angle       3.68709 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 114
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: A  212 LYS cc_start: 0.7770 (tttm) cc_final: 0.6956 (mtpt)
REVERT: B  403 ASP cc_start: 0.7696 (t0) cc_final: 0.7365 (t0)
  outliers start: 31
  outliers final: 20
  residues processed: 129
  average time/residue: 0.0793
  time to fit residues: 15.0526
Evaluate side-chains
  125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 427 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.118771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.105616 restraints weight = 15439.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.108757 restraints weight = 6764.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.110711 restraints weight = 3761.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.111828 restraints weight = 2488.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.112675 restraints weight = 1913.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9153  Z= 0.126
  Angle     :  0.564   9.723  12374  Z= 0.273
  Chirality :  0.040   0.150   1466
  Planarity :  0.003   0.030   1552
  Dihedral  :  8.995 126.464   1314
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 13.50 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.26), residues: 1144
  helix:  2.04 (0.20), residues: 730
  sheet:  0.05 (0.61), residues: 70
  loop : -0.87 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.007   0.001   TYR A 572 
 PHE   0.012   0.001   PHE A 319 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.016   0.002   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9153)
  covalent geometry    : angle       0.56411 (12374)
  hydrogen bonds       : bond        0.04046 (  552)
  hydrogen bonds       : angle       3.66353 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8336 (tm-30)
REVERT: A  212 LYS cc_start: 0.7650 (tttm) cc_final: 0.7251 (ttpt)
REVERT: B  210 MET cc_start: 0.9210 (tmm) cc_final: 0.8888 (tmm)
REVERT: B  403 ASP cc_start: 0.7684 (t0) cc_final: 0.7363 (t0)
  outliers start: 23
  outliers final: 20
  residues processed: 122
  average time/residue: 0.0826
  time to fit residues: 14.7405
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 108 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 109 optimal weight:    4.9990
   chunk 87 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.116204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.103336 restraints weight = 15362.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.106370 restraints weight = 6753.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.108266 restraints weight = 3776.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.109380 restraints weight = 2510.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110165 restraints weight = 1926.098|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9153  Z= 0.157
  Angle     :  0.593  10.160  12374  Z= 0.288
  Chirality :  0.041   0.145   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.737 125.884   1314
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 13.91 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.26), residues: 1144
  helix:  2.01 (0.20), residues: 722
  sheet: -0.08 (0.59), residues: 72
  loop : -0.89 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 102 
 TYR   0.008   0.001   TYR A 572 
 PHE   0.025   0.001   PHE A 288 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.010   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9153)
  covalent geometry    : angle       0.59288 (12374)
  hydrogen bonds       : bond        0.04269 (  552)
  hydrogen bonds       : angle       3.74416 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: A  212 LYS cc_start: 0.7736 (tttm) cc_final: 0.7418 (mtpp)
REVERT: A  535 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8376 (pt)
REVERT: B  210 MET cc_start: 0.9208 (tmm) cc_final: 0.8897 (tmm)
REVERT: B  403 ASP cc_start: 0.7744 (t0) cc_final: 0.7437 (t0)
  outliers start: 24
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0765
  time to fit residues: 13.9712
Evaluate side-chains
  125 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  100 MET
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 108 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0050
   chunk 36 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.119061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.105870 restraints weight = 15317.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.108981 restraints weight = 6797.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.110947 restraints weight = 3819.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.112155 restraints weight = 2531.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.112958 restraints weight = 1913.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9153  Z= 0.115
  Angle     :  0.560  10.045  12374  Z= 0.272
  Chirality :  0.040   0.138   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.545 124.515   1314
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 14.93 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.26), residues: 1144
  helix:  2.07 (0.20), residues: 734
  sheet:  0.14 (0.62), residues: 70
  loop : -0.90 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 102 
 TYR   0.007   0.001   TYR A 572 
 PHE   0.011   0.001   PHE A 319 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.011   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9153)
  covalent geometry    : angle       0.55979 (12374)
  hydrogen bonds       : bond        0.04008 (  552)
  hydrogen bonds       : angle       3.63349 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: A  212 LYS cc_start: 0.7725 (tttm) cc_final: 0.7515 (mtpp)
REVERT: A  535 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (pt)
REVERT: B  159 MET cc_start: 0.8748 (tmm) cc_final: 0.8527 (tmm)
REVERT: B  210 MET cc_start: 0.9190 (tmm) cc_final: 0.8892 (tmm)
REVERT: B  403 ASP cc_start: 0.7659 (t0) cc_final: 0.7373 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 123
  average time/residue: 0.0760
  time to fit residues: 14.1318
Evaluate side-chains
  126 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  312 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    0.2980
   chunk 27 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0270
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
A 562 HIS
B 568 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.120439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.107200 restraints weight = 15226.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.110318 restraints weight = 6736.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112276 restraints weight = 3778.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.113519 restraints weight = 2511.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.114333 restraints weight = 1893.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9153  Z= 0.113
  Angle     :  0.571  10.201  12374  Z= 0.274
  Chirality :  0.040   0.140   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.429 123.614   1314
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.24 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.66 (0.26), residues: 1144
  helix:  2.08 (0.20), residues: 734
  sheet:  0.21 (0.62), residues: 70
  loop : -0.90 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 102 
 TYR   0.007   0.001   TYR A 572 
 PHE   0.028   0.001   PHE A 288 
 TRP   0.006   0.001   TRP B  17 
 HIS   0.012   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 9153)
  covalent geometry    : angle       0.57112 (12374)
  hydrogen bonds       : bond        0.03922 (  552)
  hydrogen bonds       : angle       3.60848 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8269 (tm-30)
REVERT: A  535 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8352 (pt)
REVERT: B   34 LEU cc_start: 0.8647 (tp) cc_final: 0.8423 (tp)
REVERT: B  159 MET cc_start: 0.8741 (tmm) cc_final: 0.8515 (tmm)
REVERT: B  237 MET cc_start: 0.8779 (tpt) cc_final: 0.8251 (tpt)
REVERT: B  403 ASP cc_start: 0.7624 (t0) cc_final: 0.7336 (t0)
  outliers start: 22
  outliers final: 20
  residues processed: 123
  average time/residue: 0.0773
  time to fit residues: 14.2652
Evaluate side-chains
  126 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  396 ASP
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 64 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.118336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105177 restraints weight = 15309.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.108289 restraints weight = 6807.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110262 restraints weight = 3824.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.111332 restraints weight = 2527.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112186 restraints weight = 1950.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9153  Z= 0.139
  Angle     :  0.592  10.227  12374  Z= 0.286
  Chirality :  0.041   0.150   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.415 122.658   1314
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.26 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.26), residues: 1144
  helix:  2.06 (0.20), residues: 722
  sheet:  0.15 (0.61), residues: 70
  loop : -0.89 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 102 
 TYR   0.014   0.001   TYR A 162 
 PHE   0.015   0.001   PHE B 265 
 TRP   0.005   0.001   TRP B  10 
 HIS   0.014   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9153)
  covalent geometry    : angle       0.59199 (12374)
  hydrogen bonds       : bond        0.04069 (  552)
  hydrogen bonds       : angle       3.68344 ( 1626)

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8498 (tm-30)
REVERT: A  212 LYS cc_start: 0.7590 (mtpp) cc_final: 0.7340 (tttm)
REVERT: A  535 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8349 (pt)
REVERT: B  159 MET cc_start: 0.8753 (tmm) cc_final: 0.8520 (tmm)
REVERT: B  403 ASP cc_start: 0.7703 (t0) cc_final: 0.7420 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 120
  average time/residue: 0.0763
  time to fit residues: 13.7174
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 109
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   51 LEU
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 MET
Chi-restraints excluded: chain A residue  535 ILE
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 91 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.117279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104210 restraints weight = 15180.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.107305 restraints weight = 6770.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109240 restraints weight = 3803.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.110449 restraints weight = 2527.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.111236 restraints weight = 1908.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9153  Z= 0.151
  Angle     :  0.607  10.296  12374  Z= 0.293
  Chirality :  0.042   0.145   1466
  Planarity :  0.003   0.032   1552
  Dihedral  :  8.399 120.881   1314
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.97 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.26), residues: 1144
  helix:  2.04 (0.20), residues: 722
  sheet:  0.10 (0.61), residues: 70
  loop : -0.89 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 102 
 TYR   0.014   0.001   TYR B 351 
 PHE   0.038   0.001   PHE A 288 
 TRP   0.006   0.001   TRP B  10 
 HIS   0.014   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 9153)
  covalent geometry    : angle       0.60684 (12374)
  hydrogen bonds       : bond        0.04218 (  552)
  hydrogen bonds       : angle       3.74010 ( 1626)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1275.31 seconds
wall clock time: 22 minutes 48.89 seconds (1368.89 seconds total)