Starting phenix.real_space_refine
on Thu Feb 13 22:01:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bcw_12145/02_2025/7bcw_12145.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bcw_12145/02_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_12145/02_2025/7bcw_12145.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bcw_12145/02_2025/7bcw_12145.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bcw_12145/02_2025/7bcw_12145.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bcw_12145/02_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-5592/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: 6.42, per 1000 atoms: 0.71
  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: 2.42
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.89
  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: 2.52

  Time building geometry restraints manager: 2.76 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:                  0.010
  Normalize map: mean=0, sd=1:             3.070
  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:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.290
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.030
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.120
-------------------------------------------------------------------------------
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  : 0.816 
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: 0.2029
  time to fit residues: 32.9595
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  : 1.069 
-------------------------------------------------------------------------------
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:    0.0470
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   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:    1.2682

-------------------------------------------------------------------------------
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 = 0.3374 r_free = 0.3374 target = 0.107111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.095023 restraints weight = 15043.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.097811 restraints weight = 6810.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.099465 restraints weight = 3874.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.0983

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= 0.239
  Angle     :  0.610   8.378  12374  Z= 0.302
  Chirality :  0.042   0.146   1466
  Planarity :  0.004   0.037   1552
  Dihedral  : 10.394 159.575   1314
  Min Nonbonded Distance : 1.909

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  7.57 %
    Favored  : 91.51 %
  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:  0.85 (0.25), residues: 1144
  helix:  1.49 (0.20), residues: 730
  sheet: -0.14 (0.62), residues: 70
  loop : -1.29 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 165 
 HIS   0.009   0.001   HIS B 568 
 PHE   0.021   0.001   PHE A  43 
 TYR   0.009   0.001   TYR A 572 
 ARG   0.005   0.000   ARG A 391 

*********************** 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
  120 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7959 (tttm) cc_final: 0.7563 (ttpt)
REVERT: B  403 ASP cc_start: 0.7716 (t0) cc_final: 0.7321 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 114
  average time/residue: 0.2265
  time to fit residues: 36.1710
Evaluate side-chains
  100 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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 17 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 21 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.113918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.101194 restraints weight = 15557.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.104176 restraints weight = 6881.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.106029 restraints weight = 3856.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9153  Z= 0.309
  Angle     :  0.627  10.345  12374  Z= 0.309
  Chirality :  0.043   0.146   1466
  Planarity :  0.003   0.033   1552
  Dihedral  : 10.257 162.675   1314
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 10.84 %
    Favored  : 87.12 %
  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:  0.93 (0.25), residues: 1144
  helix:  1.58 (0.20), residues: 730
  sheet: -0.28 (0.60), residues: 70
  loop : -1.28 (0.32), residues: 344

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   0.013   0.001   PHE B  56 
 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
  122 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 1.071 
Fit side-chains
REVERT: A  212 LYS cc_start: 0.7989 (tttm) cc_final: 0.7624 (ttpt)
REVERT: B  403 ASP cc_start: 0.7815 (t0) cc_final: 0.7430 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 113
  average time/residue: 0.2102
  time to fit residues: 33.5319
Evaluate side-chains
  112 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 VAL
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  245 VAL
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 81 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 112 optimal weight:    0.0980
   chunk 113 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9990
   chunk 4 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0570
   overall best weight:    0.4698

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.119622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.106843 restraints weight = 15121.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.109926 restraints weight = 6609.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.111866 restraints weight = 3678.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9153  Z= 0.150
  Angle     :  0.543   8.326  12374  Z= 0.266
  Chirality :  0.040   0.135   1466
  Planarity :  0.003   0.032   1552
  Dihedral  :  9.882 155.665   1314
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 12.07 %
    Favored  : 86.09 %
  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:  1.33 (0.26), residues: 1144
  helix:  1.87 (0.20), residues: 730
  sheet: -0.07 (0.61), residues: 70
  loop : -1.09 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 165 
 HIS   0.010   0.001   HIS B 568 
 PHE   0.020   0.001   PHE A 319 
 TYR   0.008   0.001   TYR A 572 
 ARG   0.003   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
  140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A   98 MET cc_start: 0.7892 (ttp) cc_final: 0.7691 (ttt)
REVERT: A  208 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: A  212 LYS cc_start: 0.7842 (tttm) cc_final: 0.6986 (mtpt)
REVERT: B  403 ASP cc_start: 0.7725 (t0) cc_final: 0.7423 (t0)
REVERT: B  427 HIS cc_start: 0.7280 (t-90) cc_final: 0.7026 (t70)
  outliers start: 18
  outliers final: 10
  residues processed: 130
  average time/residue: 0.1826
  time to fit residues: 34.9215
Evaluate side-chains
  114 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
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 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  312 MET
Chi-restraints excluded: chain B residue  396 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 61 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 75 optimal weight:    0.5980
   overall best weight:    1.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.114479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.101518 restraints weight = 15438.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.104553 restraints weight = 6851.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106451 restraints weight = 3852.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   9153  Z= 0.296
  Angle     :  0.617   8.676  12374  Z= 0.300
  Chirality :  0.042   0.147   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.896 155.667   1314
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 13.39 %
    Favored  : 83.95 %
  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:  1.26 (0.25), residues: 1144
  helix:  1.83 (0.20), residues: 730
  sheet: -0.15 (0.61), residues: 70
  loop : -1.12 (0.33), residues: 344

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   0.014   0.001   PHE A 319 
 TYR   0.008   0.001   TYR A 572 
 ARG   0.004   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
  129 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 1.044 
Fit side-chains
REVERT: A   98 MET cc_start: 0.8068 (ttp) cc_final: 0.7801 (ttt)
REVERT: A  212 LYS cc_start: 0.7873 (tttm) cc_final: 0.7525 (ttpt)
REVERT: B  159 MET cc_start: 0.8643 (tmm) cc_final: 0.8439 (tmm)
REVERT: B  210 MET cc_start: 0.9214 (tmm) cc_final: 0.8958 (tmm)
REVERT: B  403 ASP cc_start: 0.7802 (t0) cc_final: 0.7522 (t0)
REVERT: B  514 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (tt0)
  outliers start: 26
  outliers final: 21
  residues processed: 116
  average time/residue: 0.1967
  time to fit residues: 33.3682
Evaluate side-chains
  124 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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  237 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  466 MET
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  158 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  514 GLU
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 106 optimal weight:    0.1980
   chunk 39 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 197 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.118444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.105444 restraints weight = 15100.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108554 restraints weight = 6665.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.110509 restraints weight = 3723.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9153  Z= 0.161
  Angle     :  0.556   9.901  12374  Z= 0.268
  Chirality :  0.040   0.137   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.635 147.220   1314
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.24 %
    Favored  : 82.82 %
  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:  1.51 (0.26), residues: 1144
  helix:  2.01 (0.20), residues: 730
  sheet:  0.00 (0.62), residues: 70
  loop : -1.01 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 165 
 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   0.002   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
  132 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.025 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8399 (tm-30)
REVERT: A  212 LYS cc_start: 0.7885 (tttm) cc_final: 0.7448 (mtpt)
REVERT: A  535 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8278 (pt)
REVERT: B  403 ASP cc_start: 0.7729 (t0) cc_final: 0.7439 (t0)
  outliers start: 19
  outliers final: 12
  residues processed: 122
  average time/residue: 0.1858
  time to fit residues: 33.0271
Evaluate side-chains
  119 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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  294 LEU
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:    0.8980
   chunk 94 optimal weight:    0.1980
   chunk 91 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0970
   chunk 22 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9980
   chunk 111 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.118419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.105328 restraints weight = 15367.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.108445 restraints weight = 6790.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.110404 restraints weight = 3801.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.1954

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= 0.173
  Angle     :  0.557   9.785  12374  Z= 0.269
  Chirality :  0.040   0.141   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.452 135.832   1314
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.05 %
    Favored  : 82.00 %
  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:  1.53 (0.26), residues: 1144
  helix:  2.01 (0.20), residues: 734
  sheet:  0.04 (0.61), residues: 70
  loop : -0.99 (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   0.011   0.001   PHE A 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.002   0.000   ARG A 102 

*********************** 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
  130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.076 
Fit side-chains
REVERT: A  162 TYR cc_start: 0.8634 (t80) cc_final: 0.8425 (t80)
REVERT: A  208 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: A  212 LYS cc_start: 0.7852 (tttm) cc_final: 0.7092 (mtpt)
REVERT: A  535 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8287 (pt)
REVERT: B  210 MET cc_start: 0.9187 (tmm) cc_final: 0.8871 (tmm)
REVERT: B  403 ASP cc_start: 0.7735 (t0) cc_final: 0.7434 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 120
  average time/residue: 0.1880
  time to fit residues: 33.3504
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  : 1.018 
-------------------------------------------------------------------------------
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0570
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7702

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

Flipped N/Q/H residues before XYZ refinement:
B 427 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 = 0.3597 r_free = 0.3597 target = 0.119051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.105874 restraints weight = 15390.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.109015 restraints weight = 6791.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.110974 restraints weight = 3790.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.2047

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= 0.164
  Angle     :  0.569  10.424  12374  Z= 0.270
  Chirality :  0.040   0.140   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  9.188 124.847   1314
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.16 %
    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:  1.66 (0.26), residues: 1144
  helix:  2.10 (0.20), residues: 734
  sheet:  0.10 (0.62), residues: 70
  loop : -0.93 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  17 
 HIS   0.012   0.001   HIS B 568 
 PHE   0.011   0.001   PHE A 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.004   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
  130 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.987 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8423 (tm-30)
REVERT: A  212 LYS cc_start: 0.7701 (tttm) cc_final: 0.7382 (ttpt)
REVERT: A  535 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8264 (pt)
REVERT: B  403 ASP cc_start: 0.7734 (t0) cc_final: 0.7439 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 120
  average time/residue: 0.1838
  time to fit residues: 32.3508
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  : 0.958 
-------------------------------------------------------------------------------
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  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  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  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:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0970
   chunk 79 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0270
   chunk 68 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.5036

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.121430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.108299 restraints weight = 15310.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111449 restraints weight = 6706.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.113451 restraints weight = 3732.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9153  Z= 0.145
  Angle     :  0.570  10.106  12374  Z= 0.270
  Chirality :  0.040   0.148   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.736 123.700   1314
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.36 %
    Favored  : 81.49 %
  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:  1.77 (0.26), residues: 1144
  helix:  2.17 (0.20), residues: 734
  sheet:  0.20 (0.62), residues: 70
  loop : -0.85 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 165 
 HIS   0.013   0.001   HIS B 568 
 PHE   0.018   0.001   PHE A 288 
 TYR   0.016   0.001   TYR B 351 
 ARG   0.003   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
  137 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 1.093 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: A  212 LYS cc_start: 0.7727 (tttm) cc_final: 0.7210 (mtpt)
REVERT: A  535 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8332 (pt)
REVERT: B   34 LEU cc_start: 0.8512 (tp) cc_final: 0.8271 (tp)
REVERT: B  403 ASP cc_start: 0.7708 (t0) cc_final: 0.7318 (t0)
  outliers start: 21
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1854
  time to fit residues: 33.8197
Evaluate side-chains
  127 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
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  535 ILE
Chi-restraints excluded: chain B residue   51 LEU
Chi-restraints excluded: chain B residue   70 VAL
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  318 LEU
Chi-restraints excluded: chain B residue  396 ASP
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:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0270
   chunk 46 optimal weight:    6.9990
   chunk 66 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9980
   overall best weight:    0.7440

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

Flipped N/Q/H residues before XYZ refinement:
B 427 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 = 0.3599 r_free = 0.3599 target = 0.116653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.104688 restraints weight = 14879.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107698 restraints weight = 6387.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.109578 restraints weight = 3493.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2279

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= 0.167
  Angle     :  0.579  10.069  12374  Z= 0.275
  Chirality :  0.040   0.156   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.511 122.733   1314
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.59 %
    Favored  : 80.67 %
  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:  1.78 (0.26), residues: 1144
  helix:  2.18 (0.20), residues: 734
  sheet:  0.22 (0.62), residues: 70
  loop : -0.87 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  10 
 HIS   0.015   0.001   HIS B 568 
 PHE   0.011   0.001   PHE A 319 
 TYR   0.012   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
  128 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 1.062 
Fit side-chains
REVERT: A  208 GLU cc_start: 0.8741 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: A  212 LYS cc_start: 0.7628 (tttm) cc_final: 0.7070 (mtpt)
REVERT: A  535 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8353 (pt)
REVERT: B   34 LEU cc_start: 0.8533 (tp) cc_final: 0.8283 (tp)
REVERT: B  403 ASP cc_start: 0.7699 (t0) cc_final: 0.7280 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 119
  average time/residue: 0.1806
  time to fit residues: 32.2162
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  : 1.041 
-------------------------------------------------------------------------------
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  394 ASP
Chi-restraints excluded: chain A residue  397 GLU
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  128 ILE
Chi-restraints excluded: chain B residue  245 VAL
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  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:    4.9990
   chunk 78 optimal weight:    0.0060
   chunk 49 optimal weight:    2.9990
   chunk 41 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.0004

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.118838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105895 restraints weight = 15406.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.108939 restraints weight = 6803.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110885 restraints weight = 3815.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.2258

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= 0.193
  Angle     :  0.586  10.169  12374  Z= 0.280
  Chirality :  0.041   0.144   1466
  Planarity :  0.003   0.031   1552
  Dihedral  :  8.386 121.594   1314
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.59 %
    Favored  : 80.16 %
  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:  1.75 (0.26), residues: 1144
  helix:  2.15 (0.20), residues: 734
  sheet:  0.18 (0.62), residues: 70
  loop : -0.88 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  10 
 HIS   0.014   0.001   HIS B 568 
 PHE   0.010   0.001   PHE A 319 
 TYR   0.018   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: 2406.26 seconds
wall clock time: 44 minutes 26.91 seconds (2666.91 seconds total)