Starting phenix.real_space_refine
on Fri Mar 14 01:33:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_12145.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_12145.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_12145.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_12145.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bcw_12145/03_2025/7bcw_12145.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.25, per 1000 atoms: 0.80
  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: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.96
  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: 2.86

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.18 -     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 579 or resid 601 through 603 or (resid 604 and ( \ 
name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ 
r name C26 or name C27 or name C28 or name C29 or name C3 or name O11 or name O1 \ 
2 or name O13 or name O14 or name O21 or name O22 or name O31))))
  selection = (chain 'B' and (resid 6 through 579 or resid 601 through 603 or (resid 604 and ( \ 
name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or name C25 o \ 
r name C26 or name C27 or name C28 or name C29 or name C3 or name O11 or name O1 \ 
2 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:             2.620
  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:             0.020
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     26.470
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.850
-------------------------------------------------------------------------------
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= 0.348
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (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
 TRP   0.010   0.002   TRP B  91 
 HIS   0.011   0.001   HIS B 568 
 PHE   0.014   0.001   PHE A  56 
 TYR   0.007   0.001   TYR A  83 
 ARG   0.009   0.001   ARG A 377 

*********************** 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  : 1.093 
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: 0.2446
  time to fit residues: 40.2410
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  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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 = 0.3368 r_free = 0.3368 target = 0.106705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.094599 restraints weight = 15063.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.097383 restraints weight = 6828.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.099114 restraints weight = 3887.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9153  Z= 0.258
  Angle     :  0.617   8.596  12374  Z= 0.306
  Chirality :  0.042   0.148   1466
  Planarity :  0.004   0.037   1552
  Dihedral  : 10.400 160.797   1314
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  :  7.87 %
    Favored  : 91.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.25), residues: 1144
  helix:  1.46 (0.20), residues: 730
  sheet: -0.18 (0.61), residues: 70
  loop : -1.31 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.008   0.001   HIS B 568 
 PHE   0.021   0.001   PHE A  43 
 TYR   0.010   0.001   TYR A 572 
 ARG   0.004   0.000   ARG B 377 

*********************** 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
  121 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 1.066 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7955 (tttm) cc_final: 0.7553 (ttpt)
REVERT: B  403 ASP cc_start: 0.7735 (t0) cc_final: 0.7337 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2764
  time to fit residues: 44.7892
Evaluate side-chains
  100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 96
  time to evaluate  : 1.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  245 VAL
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 17 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:   10.0000
   chunk 51 optimal weight:    0.6980
   chunk 111 optimal weight:    2.9990
   chunk 93 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 21 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.116464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.103537 restraints weight = 15429.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.106601 restraints weight = 6780.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.108515 restraints weight = 3786.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9153  Z= 0.214
  Angle     :  0.581  10.685  12374  Z= 0.285
  Chirality :  0.041   0.148   1466
  Planarity :  0.003   0.032   1552
  Dihedral  : 10.098 159.043   1314
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.43 %
    Favored  : 87.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.25), residues: 1144
  helix:  1.74 (0.20), residues: 718
  sheet: -0.11 (0.61), residues: 70
  loop : -1.12 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 165 
 HIS   0.008   0.001   HIS B 568 
 PHE   0.021   0.001   PHE A  43 
 TYR   0.009   0.001   TYR A 572 
 ARG   0.003   0.000   ARG B 377 

*********************** 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
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.968 
Fit side-chains
REVERT: A  200 MET cc_start: 0.9313 (tpp) cc_final: 0.9097 (tpt)
REVERT: A  208 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8049 (tm-30)
REVERT: A  212 LYS cc_start: 0.7909 (tttm) cc_final: 0.7023 (mtpt)
REVERT: B  210 MET cc_start: 0.9224 (tmm) cc_final: 0.8948 (tmm)
REVERT: B  403 ASP cc_start: 0.7788 (t0) cc_final: 0.7358 (t0)
REVERT: B  516 GLU cc_start: 0.7448 (tt0) cc_final: 0.7231 (tt0)
  outliers start: 21
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1956
  time to fit residues: 34.4369
Evaluate side-chains
  113 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  128 ILE
Chi-restraints excluded: chain A residue  237 MET
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   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  312 MET
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9990
   chunk 86 optimal weight:    0.5980
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.115522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.102692 restraints weight = 15396.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105712 restraints weight = 6792.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.107605 restraints weight = 3803.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.1465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9153  Z= 0.252
  Angle     :  0.590   9.687  12374  Z= 0.288
  Chirality :  0.041   0.144   1466
  Planarity :  0.003   0.032   1552
  Dihedral  :  9.971 157.897   1314
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 12.37 %
    Favored  : 85.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.25), residues: 1144
  helix:  1.82 (0.20), residues: 718
  sheet: -0.17 (0.60), residues: 70
  loop : -1.09 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  10 
 HIS   0.009   0.001   HIS B 568 
 PHE   0.015   0.001   PHE A 319 
 TYR   0.008   0.001   TYR A 572 
 ARG   0.005   0.000   ARG A 102 

*********************** 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
  130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7845 (tttm) cc_final: 0.7420 (ttpt)
REVERT: B  403 ASP cc_start: 0.7792 (t0) cc_final: 0.7512 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1890
  time to fit residues: 33.1671
Evaluate side-chains
  113 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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  388 LEU
Chi-restraints excluded: chain A residue  397 GLU
Chi-restraints excluded: chain A residue  402 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  320 THR
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    0.6980
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.3579 r_free = 0.3579 target = 0.117661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.104707 restraints weight = 15271.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.107804 restraints weight = 6690.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.109708 restraints weight = 3720.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9153  Z= 0.178
  Angle     :  0.566   9.858  12374  Z= 0.275
  Chirality :  0.040   0.139   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.775 152.279   1314
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 14.42 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.26), residues: 1144
  helix:  1.95 (0.20), residues: 718
  sheet:  0.01 (0.61), residues: 70
  loop : -1.01 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 165 
 HIS   0.009   0.001   HIS B 568 
 PHE   0.015   0.001   PHE A 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 102 

*********************** 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
  134 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.058 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8176 (tm-30)
REVERT: A  212 LYS cc_start: 0.7835 (tttm) cc_final: 0.7102 (mtpt)
REVERT: B  210 MET cc_start: 0.9196 (tmm) cc_final: 0.8907 (tmm)
REVERT: B  403 ASP cc_start: 0.7761 (t0) cc_final: 0.7460 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 123
  average time/residue: 0.1887
  time to fit residues: 34.3709
Evaluate side-chains
  117 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
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  128 ILE
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  108 MET
Chi-restraints excluded: chain B residue  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  422 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN
B 305 ASN
B 427 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.118332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.105367 restraints weight = 15129.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.108447 restraints weight = 6698.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110394 restraints weight = 3747.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8347
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9153  Z= 0.166
  Angle     :  0.559   9.729  12374  Z= 0.271
  Chirality :  0.040   0.151   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.572 142.636   1314
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.44 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.26), residues: 1144
  helix:  2.01 (0.20), residues: 730
  sheet:  0.13 (0.62), residues: 70
  loop : -0.98 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  17 
 HIS   0.010   0.001   HIS B 568 
 PHE   0.014   0.001   PHE A 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 102 

*********************** 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: 22
    poor density    : 113
  time to evaluate  : 1.186 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8616 (t80) cc_final: 0.8386 (t80)
REVERT: A  208 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8364 (tm-30)
REVERT: A  212 LYS cc_start: 0.7743 (tttm) cc_final: 0.7314 (ttpt)
REVERT: A  535 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8268 (pt)
REVERT: B  159 MET cc_start: 0.8691 (tmm) cc_final: 0.8470 (tmm)
REVERT: B  210 MET cc_start: 0.9203 (tmm) cc_final: 0.8934 (tmm)
REVERT: B  403 ASP cc_start: 0.7737 (t0) cc_final: 0.7436 (t0)
  outliers start: 22
  outliers final: 16
  residues processed: 124
  average time/residue: 0.2287
  time to fit residues: 41.6301
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
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  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  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 7 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0060
   chunk 22 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.7996

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.118714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.105570 restraints weight = 15358.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.108715 restraints weight = 6780.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.110655 restraints weight = 3780.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9153  Z= 0.166
  Angle     :  0.563  10.544  12374  Z= 0.270
  Chirality :  0.040   0.141   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.293 125.000   1314
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 15.95 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.26), residues: 1144
  helix:  2.05 (0.20), residues: 734
  sheet:  0.19 (0.62), residues: 70
  loop : -0.94 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  10 
 HIS   0.010   0.001   HIS B 568 
 PHE   0.013   0.001   PHE A 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.003   0.000   ARG A 377 

*********************** 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
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8625 (t80) cc_final: 0.8356 (t80)
REVERT: A  208 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8273 (tm-30)
REVERT: A  535 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8260 (pt)
REVERT: B  210 MET cc_start: 0.9196 (tmm) cc_final: 0.8926 (tmm)
REVERT: B  403 ASP cc_start: 0.7740 (t0) cc_final: 0.7449 (t0)
  outliers start: 21
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1896
  time to fit residues: 33.6717
Evaluate side-chains
  122 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 17 optimal weight:    0.3980
   chunk 29 optimal weight:    5.9990
   chunk 104 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.7584

-------------------------------------------------------------------------------
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 = 0.3601 r_free = 0.3601 target = 0.119383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.106186 restraints weight = 15368.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.109311 restraints weight = 6803.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111303 restraints weight = 3808.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9153  Z= 0.166
  Angle     :  0.566   9.913  12374  Z= 0.271
  Chirality :  0.040   0.138   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.015 124.373   1314
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 17.08 %
    Favored  : 80.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1144
  helix:  2.07 (0.20), residues: 734
  sheet:  0.22 (0.62), residues: 70
  loop : -0.89 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.011   0.001   HIS B 568 
 PHE   0.012   0.001   PHE A 319 
 TYR   0.017   0.001   TYR B 351 
 ARG   0.003   0.000   ARG A 102 

*********************** 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
  131 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.026 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7628 (mtpp) cc_final: 0.7001 (ttpt)
REVERT: A  535 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8253 (pt)
REVERT: B  159 MET cc_start: 0.8692 (tmm) cc_final: 0.8487 (tmm)
REVERT: B  210 MET cc_start: 0.9184 (tmm) cc_final: 0.8907 (tmm)
REVERT: B  403 ASP cc_start: 0.7737 (t0) cc_final: 0.7455 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1860
  time to fit residues: 32.7244
Evaluate side-chains
  121 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
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  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  312 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  505 ASP
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 92 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.118593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.105531 restraints weight = 15391.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.108598 restraints weight = 6814.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.110537 restraints weight = 3818.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.2141

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= 0.187
  Angle     :  0.581  10.108  12374  Z= 0.281
  Chirality :  0.041   0.140   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.733 123.525   1314
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.48 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1144
  helix:  2.05 (0.20), residues: 734
  sheet:  0.18 (0.62), residues: 70
  loop : -0.86 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  10 
 HIS   0.012   0.001   HIS B 568 
 PHE   0.012   0.001   PHE A 319 
 TYR   0.018   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 102 

*********************** 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
  129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.130 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8231 (tm-30)
REVERT: A  212 LYS cc_start: 0.7597 (mtpp) cc_final: 0.7194 (mtpt)
REVERT: A  535 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8311 (pt)
REVERT: B   34 LEU cc_start: 0.8653 (tp) cc_final: 0.8424 (tp)
REVERT: B  159 MET cc_start: 0.8698 (tmm) cc_final: 0.8462 (tmm)
REVERT: B  210 MET cc_start: 0.9187 (tmm) cc_final: 0.8888 (tmm)
REVERT: B  403 ASP cc_start: 0.7757 (t0) cc_final: 0.7479 (t0)
  outliers start: 20
  outliers final: 17
  residues processed: 119
  average time/residue: 0.1804
  time to fit residues: 32.3556
Evaluate side-chains
  123 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 105
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
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  388 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  312 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  505 ASP
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 69 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 405 HIS
B 427 HIS
B 568 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.118221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.105109 restraints weight = 15380.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.108226 restraints weight = 6812.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110176 restraints weight = 3808.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9153  Z= 0.196
  Angle     :  0.591  10.140  12374  Z= 0.285
  Chirality :  0.041   0.157   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.524 122.294   1314
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 17.28 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.26), residues: 1144
  helix:  2.09 (0.20), residues: 722
  sheet:  0.18 (0.62), residues: 70
  loop : -0.85 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  10 
 HIS   0.014   0.001   HIS B 568 
 PHE   0.022   0.001   PHE A 288 
 TYR   0.016   0.001   TYR A 162 
 ARG   0.004   0.000   ARG A 102 

********************** 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
  129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: A  212 LYS cc_start: 0.7629 (mtpp) cc_final: 0.7277 (ttpt)
REVERT: A  535 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8347 (pt)
REVERT: B   34 LEU cc_start: 0.8659 (tp) cc_final: 0.8423 (tp)
REVERT: B  159 MET cc_start: 0.8707 (tmm) cc_final: 0.8469 (tmm)
REVERT: B  210 MET cc_start: 0.9156 (tmm) cc_final: 0.8841 (tmm)
REVERT: B  403 ASP cc_start: 0.7761 (t0) cc_final: 0.7378 (t0)
  outliers start: 21
  outliers final: 17
  residues processed: 119
  average time/residue: 0.1791
  time to fit residues: 32.0969
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
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  388 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  312 MET
Chi-restraints excluded: chain B residue  390 THR
Chi-restraints excluded: chain B residue  422 VAL
Chi-restraints excluded: chain B residue  505 ASP
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 47 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 74 optimal weight:    0.6980
   chunk 63 optimal weight:    0.3980
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3620 r_free = 0.3620 target = 0.120676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.107648 restraints weight = 15348.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.110737 restraints weight = 6766.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.112698 restraints weight = 3781.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.2301

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= 0.166
  Angle     :  0.578   9.671  12374  Z= 0.279
  Chirality :  0.040   0.149   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.362 121.028   1314
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 18.10 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.26), residues: 1144
  helix:  2.13 (0.20), residues: 722
  sheet:  0.26 (0.63), residues: 70
  loop : -0.83 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  17 
 HIS   0.015   0.001   HIS B 568 
 PHE   0.012   0.001   PHE A 319 
 TYR   0.017   0.001   TYR B 351 
 ARG   0.004   0.000   ARG A 102 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2608.30 seconds
wall clock time: 47 minutes 48.84 seconds (2868.84 seconds total)